The Lonely Angel
by cariaudry
Summary: Something has gone wrong on Earth. Valentine didn't lose the Mortal War and has claimed lordship over the shadowhunters. In the bitter aftermath, he sends Jace and Clary back to New York as punishment, keeping them as his prisoners, and it's not a pleasant life. However, when things go wrong on Earth, a certain blue police call box is bound to appear, and the Doctor with it.
1. The Spoils of War

The Spoils of War

_Night will fall and drown the sun, when a good man goes to war_

_-Steven Moffat _

The bed groaned loudly as Clary rolled over and she froze in mute horror. She waited on baited breath, listening for the sound of a waking person coming to investigate what a young girl was doing awake at such a late hour. The seconds became minutes and Clary began to suspect that no one was coming for her, and gradually, she worked her nerve up to swing her legs around and place two unsteady feet on the floor. The cold floor stung the sore pads of her feet, but she breathed out and forced herself to move on.

_Turn the knob slowly, it squeaks,_ Clary told herself as she approached the door to her bedroom. _The first floorboard on the right is loose, don't trip on it. _

The silent orders were the only thing that was keeping Clary from racing back to her bed in a panic and hiding under the covers. Her mind was in a torrent, screaming at her to turn around before Valentine, or worse, caught her out of bed, but a small voice kept telling her to get up and go. It was weak, but the growling in her stomach was lending it strength.

_They'll never know, _the voice whispered, _if you slip downstairs for a quick snack. Just some bread with butter, just some water, maybe a handful of baby carrots; just enough to hold you over until lunch at school. Just enough for tomorrow._

While she'd been having the conversation with herself, Clary had opened the door to her room, carefully avoiding the loose board, and was already at the platform before the stairs. The realization that she was directly disobeying her father made her mind reel and she felt dizzy-or, maybe it was the three days she'd gone with no food and water. Either way, Clary felt herself sink down to a childish squat on the edge of the stairs, clutching her messy hair.

_Go back, just go back and crawl into bed, cover yourself up with the blanket and pretend this never happened. Your father doesn't have to know, no one has to know what you did,_ her reasonable self whispered.

But the hunger that had driven Clary from her bed in the first place was too powerful now. She sat on the edge of the stairs, and toes first, placed her feet down on the first stair. She shifted all the weight onto her hands to silence the sound her body would make on the stairs, and lifted herself down to the stair. Toe by two, stair by stair, Clary made her way in the manner of a small child sneaking down the stairs, until she landed on the base.

Clary's eyes darted back up the stairs, a sudden fear gripping her that someone would be standing there, staring down at her like a vengeful God. However, the stairwell was dark and still, she heard no footsteps. She no longer heard the warnings from her mind, only the growling in her stomach urging her on and the little crying _go, go, go!_

For a moment, Clary debated standing up and running for the kitchen, but she almost at once decided against it. She made too much noise on two feet, and, if someone did wake up, her standing up would be spotted at once. Dejectedly, Clary began to crawl on her hands and knees toward the kitchen tile floor.

_This is so degrading, _Clary thought as she crawled under the huge dining room table and huddled there a moment to gather her wits. _You're crawling around like some animal, scrounging for scraps because your own family won't feed you. _While this was true, again, Clary's little voice answered, _It doesn't matter what you have to do, it doesn't matter how low you have to sink, you need to survive. Just get to the kitchen and get the food. You can stroke your ego later. _

A bitter smile curled Clary's lips; she was never going to stroke her ego again. But, the voice had been enough to encourage her to keep moving. Clary listened for a moment longer, checking for signs of life in the house, but there were none, and she moved on again. Out from under the table she crawled, and quietly, like a little mouse, she found her way to tiled kitchen floor. Shaking with anticipation and reveling in her own success, Clary drew herself up against the cabinets on the floor and sighed.

_Go! Go to the fridge-open the door slowly, always slowly!-and get the bread and carrots. _Clary surveyed the kitchen around her, and spotted, opposite the little island, the imposing sub-zero refrigerator. _Pour a glass of water from the picture inside. A cold, cold glass of water. Your throat is so dry…_

Clary moved like a madness had consumed her. She took the long way around the island, just in case someone woke up, and arrived at the refrigerator, arms trembling. It had been three days since her last meal, three days since her last drink, three days of compounding, horrible longing, and now, here was her prayer answered.

The door opened silently, and the spill of light illuminated Clary's face. When she looked up from her crouch on the floor, she beheld shelves and shelves of fresh vegetables and fruits, packed lunch meats, cans of soda and juice, even chocolate éclairs from last night's dinner she had been dismissed from. But Clary knew what she was there for.

_Take the bread and the carrots, nothing that can be noticed as missing. Don't touch the meat, you'll leave finger prints all over the place. He'll know…_Clary's hand shot out and retrieved a loaf of fresh bakery bread and a bag of baby carrots. She reached across her to the island and removed a glass from the rack beneath it, carefully, and poured herself a tall glass of fresh, chilly water. Swiftly, she shut the door and settled onto the floor again, hunched over her meager meal of bread, carrots and water like a snarling animal.

_Eat, eat, eat! _ordered the voice, and Clary fell on the meal ravenously, her heart exploding with the pleasure of the food.. _Don't stop, be quick, don't leave crumbs, but eat!_ Sitting there, feeling her belly fill, Clary decided she'd made a good choice after all. She shouldn't have been so worried. _No one will ever know, it's our little secret. Eat your fill, put the food away, clean the mess, and then we'll crawl back in bed with a full stomach. No one needs to know-_

"It appears I have a rat infestation," drawled a voice from right above Clary's head.

The food in Clary's mouth turned to ash and her heart stopped beating. Trembling, now in fear, Clary slowly looked up and behind her, wishing it was all her imagination. At the sight of her father, Clary's hands convulsed and she dropped the bread she'd been eating and glass of water in her hand. The glass broke into jagged little bits and the water seeped into her nightgown.

"F-father," Clary stuttered, thinking as fast as she could. Unfortunately, while the little voice had been so encouraging before, it had now abandoned her, leaving her, like usual, to deal with the consequences of reality. "I-I didn't know you were awake."

"Hmm," hummed Valentine, flicking the light on and surveying Clary with a critical eye. "No, not a rat, too timid for a rat. Maybe just a mouse."

"I didn't hear you," she said, finding her voice.

"I'm sure you're most disappointed in that, aren't you?" Valentine asked, a strange smile turning the corner of his lip up. "Perhaps, had you heard me, you might have scurried off to your room, tail between your legs, but a belly full of crumbs to keep you content, eh?"

"No," said Clary, shaking her head. "I was just eating some bread and you surprised me-"

"I bet I did," Valentine cut across her, which was good, since Clary had no idea where she was going with it. "Now, Clarissa, I told you that you weren't allow to eat, that you're abysmal grade on your math exam had earned you that punishment, but that, if your English paper grade was sufficient, I would let you have dinner with us on Monday. Now, here I find you, eating food off the floor like some animal, and what am I supposed to think?"

"Father," Clary began in a weak voice. She had learned long ago that arguing with him, with showing him any kind of will, could easily land her on the balcony of their apartment, tied to the railing in the cold. "I haven't eaten in days, and I didn't think I could last till Monday."

"And whose fault is that?" Valentine knelt down beside Clary, eyebrows raised in a question. "It's certainly not my fault, is it? I simply told you the consequences of your actions; if anyone is at fault, it's you. You're the one who failed-"

"I got a B!"

"And I'm supposed to be impressed with that?" Valentine asked sharply. "I expect excellence in all fields, and you think coming home with a B is acceptable, especially since there were _Mundanes_ who got A's?"

"But, I studied-"

"Poorly," he finished. "Now, you are simply dealing with the consequences of your actions, and you appear to be doing that poorly, too. I'm not impressed by this, and neither am I sympathetic."

"Clary?" Valentine snapped about and the same time Clary moaned. "What are you doing to her?"

"Ah, Jace," Valentine said, his eyes glowing. "I should have guessed you'd come down here the moment you heard your little love's voice. How very sweet."

Jace, standing in his pajamas with his tangled hair and his wide eyes, made Clary want to cry. She had never wanted him to come down here. She knew if Jace found her in danger of her father, he'd intervene, and then he'd be punished too. Jace, who was still allowed to eat, would lose those privileges as quickly as she did if he wasn't careful. It was why she had been so careful in the first place; forget waking her father, it was Jace who could hear a pin drop.

Jace took in the sight of Clary huddled over a pile of mushy bread and knew at once what he'd walked in on. "I thought I heard something, and came down to see what it was."

"Well, you certainly found something, didn't you?" Valentine asked, and his hand roved up to grasp a handful of Clary's hair. "What do you think, a mouse or a rat?"

Jace didn't even blink he was so fast. "I sent her down. I wasn't feeling well, so I asked Clary to go down and get me some bread and water. If she's done anything wrong, it should be me who's punished for sending her in the first place-"

"Jace!" Clary cried.

"Liar," Valentine said simply, and stood up, tossing Clary down into the pile of soggy bread. "I found her with a mouth full of bread, stuffing her face."

"I don't deny that," Jace answered. "I'm just saying that it's my fault. I knew Clary wasn't allowed to eat, I knew she was starving, but I still asked her to go anyway. I sent her into temptation. I should take responsibility for it."

"How very mature of you," mused Valentine, staring down into Jace's bold eyes. "But I know you're lying. Not because of any tells, just because, where my daughter is concerned, you always lie for her."

"I'm not lying-"

"Yes, you are!" Clary snarled. "Don't listen to him, Father. I came down here on my own, it was all me, Jace had nothing to do with it. Just leave him out of it."

Valentine gestured to Clary, while speaking to Jace. "My daughter seems quite adamant that you have nothing to do with this, and that I should send you to your room to wait."

"She's just protecting me. She thinks you'll stop feeding me if I help her," Jace shrugged.

"She's not wrong," Valentine replied.

"Regardless," Jace pressed on. "I sent her down here. This is my fault, and if anyone is to blame for this, it's me."

"He's lying," Clary moaned, and she felt her hand helplessly pluck the hem of her father's pants. "He's just trying to protect _me_. Please, just send him back to bed and deal with me."

Valentine gave his daughter a look filled with disgust. "You're pathetic, Clarissa. Sitting in a pile of garbage food, begging at my feet; you make me sick to call you my daughter." Clary didn't care what her father called her; all that mattered was that he send Jace away. "However, I have more pressing matters to deal with. You say Jace lies, Jace says you lie, and neither of you is willing to admit to the truth. I see only one option."

"I'm telling you the truth!" Clary pressed.

"Clary, stop lying," Jace growled under his breath.

"I can only assume you are both lying, and so, you will both be punished." Valentine kicked Clary away. "Clary, clean this mess and then go to the bathroom and take your nightgown off. I'll meet you there in ten minutes. Jace," and here, he shot a sneer at the boy, "no food or water for three days."

Jace seemed more upset with Clay's punishment than his own. "I'll take Clary's half as well," he offered, picking up a rag from the counter. "It will hurt her just as much if she sees me."

Valentine snapped the cloth from his hand and threw it at Clary with unnecessary force. "Go to your room, Jace, and stay there. If I find that you've left for anything, you'll get a whipping for your pains."

Jace's eyes found Clary's and he looked suddenly desperate. "Please, Valentine, Clary is already too weak, and she hasn't eaten in days."

Slowly, prowling forward, Valentine drew level with Jace. "I'll only tell you once to go to your room, boy." And, while still holding Jace's eye, he lifted his foot up and then brought it down on Clary's right hand. She screamed and Jace cried in horror. "Do I need to repeat myself?"

Though Jace wanted to stay and protect Clary, he knew how pointless it was going to be to linger. "I'll wait up," he told her, and then returned to his room.

Valentine remained, and he watched while Clary scrubbed up the soiled floor. "This is all you're good for. Ruined by your upbringing." Then he left her there to clean.

Though Clary tried to take her time, though she made a point of scrubbing the cracks in the floor, she knew that nothing was going to stop the clock from ticking her doom. When there was nothing left for her to clean, Clary drew herself up, and marched up the stairs, passing by the room she and Jace shared, wishing she had just gone back to bed, and turned down the hall to the bathroom.

The light was on, the fan going, and Clary felt her stomach turn like she was going to be sick. Valentine wasn't there yet, but Clary didn't think she wanted to risk his wrath any more that night, and she crossed the fuzzy carpets and tiled floors to the bathtub where she slipped out of her nightgown and sat on the rim. As the minutes ticked by, Clary shivered in nothing but her underwear, and hugged herself tighter, longing for the blankets on her bed. What she wouldn't give to be back there now.

When she heard the bathroom door close and lock, she knew Valentine was there; when she heard the sound of leather on the marble sink, she flinched. "Now, first things first; come over to the toilet."

Clary shot a look over her shoulder at her father, who was watching her with pitiless eyes. "I'm not dressed."

"I'm not interested," he said simply. "Sit in front of the toilet and give back what you stole."

Still hugging herself under the stony eye of her father, Clary knelt before the toilet and waited. She felt the presence of her father behind her, and then his arms wrap about her. One of his hands gripped her chin, the other was holding the end of her toothbrush. Clary watched, dreading what he was going to do, and she thought a few more minutes like this and the toothbrush would be unnecessary.

"I'm going to do this once," Valentine said, jerking Clary back into position when she tried to shy away from the toothbrush, "and then you're going to do it twice, to show me you understand."

Clary groaned, but Valentine squeezed his fingers, forcing her mouth to open, and shoved her toothbrush down her throat until she lurched forward, vomiting. Valentine held her over the toilet bowl, shaking her by her hair as if he was going to shake the food out, and Clary looked at the partially digested bits of bread and carrot. After a minute, he stopped shaking her, slammed the toothbrush in her hand, and then sat on the rim of the bathtub, waiting for her to complete the rest.

By the end, Clary's eyes were welling with tears, her throat burning with the acid that had come up. Valentine had emptied her stomach of food on his first go, and the last two had simply brought up blood and stomach acid, leaving her feeling raw and empty. She dropped the toothbrush on the floor and leaned on the bowl, unable to stop the shaking that was consuming her.

"Now, come here and lean over the tub," Valentine ordered, standing and retrieving his belt. "You returned what you took, but now you have to be punished for taking it in the first place."

Again, Clary thought fear might make her vomit, but this wasn't her first time playing this game. Clary clambered over to the bathtub and leaned over the rim, exposing her back to her father's mercy. It didn't take long for her father to begin, and, luckily, for him to end. It was only five lashes this time, one five welts on her back, only a single minute of pain. When it was over, Clary let out the ragged cry she'd been holding back.

"You're lucky all you got your hands on was some bread. If I'd caught you with meat in your mouth, we'd still be at it," Valentine informed her tonelessly as he washed the blood off the belt. "Get back to your room and stay there until I call you and Jace down. If I hear a whisper of this to your mother, I'll see you and Jace both whipped within an inch of your lives."

Stumbling into her nightgown, Clary nodded, and then walked stiltedly back to her bedroom. She held herself awkwardly, feeling pain lace up her back at every step, and when she had to open the door, the very movement sent a spike of pain from her stretched arm up her back. She didn't have to suffer long though, since the moment the door swung to, Jace was there, catching her as she fell.

"Clary, why did you do that?" Jace moaned as he very carefully picked her up and rested her over his shoulder so as not to touch the whip lashes. "Why would you sneak down there? I begged you not to."

Clary hated when Jace sounded like this, so miserable and helpless, like her actions were somehow his fault. When he placed her gently on the bed, Clary caught his wrist. "I was so hungry, and I just couldn't risk telling you. I knew you'd try and stop me, and if I got caught you'd be in trouble."

Jace cupped Clary's face in his hands. "You don't worry about me, alright, Clary? I know how to handle Valentine, and I know how to handle pain; I've had both of them since I was a kid. Do you think I don't feel your pain? Do you think I just got back in bed and waited for you to show up?" Jace kissed Clary passionately. "Don't _ever_ do that again."

Clary let the kiss linger. "It doesn't matter now," she said bitterly. "Now you're the one who has to starve."

"Three days is barely anything, besides, I'll eat small things at school." Jace motioned for Clary to lie down as the dug around under their bed. "I take it Valentine made you throw up?"

Clary sighed. "How did you know?"

"I've been there, and it just means I'll have to be careful about what I eat." Jace emerged with a simple first aid kit. "I wish he'd let me have my stele back; for now you'll just have to make do with alcohol and bandages."

Unable to repress a shudder, Clary shimmied out of her nightgown again, revealing her bare backside to Jace. He admired it in the moonlight. "I'm surprised Valentine lets us stay together. You think he'd keep a closer watch over his daughter than to let her shack up with a notorious player."

Though she sensed the joke, Clary shook her head. "It's punishment, Jace, he knows that when I'm hurt you'll see it, and when you're hurt, I'll see it."

"Whatever the reason, I'm grateful I get to curl up beside you at night," said Jace solemnly, and then placed his palm on her hip in warning. "This is going to hurt."

"I know," she murmured, and bit down on the pillowed as Jace began to apply alcohol to the open cuts on her back.

It didn't take long for Jace's practiced hands to clean the five lashes and apply anti-septic bandages, and he paused, his hand wavering over the rolls of gauze. "I can wrap the wounds if you want, but you'll have to sit up…" his voice trailed off and Clary knew why. They had been living in the same house, sharing the room, sleeping in the same bed for almost five months now, but Jace, always a gentlemen, and Clary, terrified of how her father might react, had never seen her naked.

"I'll sit the other way," Clary said, hoping the moonlight would bleach out the color of her blush. Jace turned his back while Clary sat on her knees and resituated herself so she sat facing the headboard. When he turned back with the gauze, Clary glanced over her shoulder and offered him her bravest smile. "This must be an ordinary teenage boy's worst nightmare?"

"When have you ever described me as ordinary?" asked Jace, and set to work wrapping her torso with gauze bandaging. It took longer than Jace liked, his hands just barely grazing her backside and never touching her front, but Clary seemed distant and unresponsive to his administrations. When he finally tied the knot, Jace found his hands were shaking just a little. "Still, I suppose I fall prey to the usual temptations."

"You can't be blamed," Clary said softly, and then, with Jace's help, settled on the bed. Jace tossed the blankets over both of them and drew Clary very gently against him. Softly, almost so softly she didn't hear him, Jace began to hum; Clary smiled at the feeling of his chest vibrating against her. "You're going to sing me to sleep?"

"Classic," Jace returned with a cocky smile. "What would you like? Bram's Lullaby?"

"That would be welcome," Clary murmured against his neck, and she slipped into sleep, tucked in the safety of Jace's arms.

As Clary was slipping into a troubled sleep, another young red-haired woman was being jerked awake by the tossing and turning of the bed beneath her. "What the hell-!"

"Listen up Ponds, we're encountering some turbulence," a ridiculously cheerful voice said over a speaker. "Nothing to be too concerned about. We might be making a landing soon." The man's voice was cut off suddenly and a groaning echoed all over the room. "Ah, yes, well, make that an emergency landing…NOW."

"Doctor!" Amy Pond cried in outrage, but she was tossed out of bed as the ground beneath her pitched forward.

"He's mad!" snarled Rory Pond, lunging after his wife and helping her to her feet on the rocking floor. "Why he has to get up to his madness at two in the morning, I'll never know."

"It's not madness!" cried the Doctor over the loudspeaker, and he was laughing like a schoolboy. "If you'll come down here, Ponds, you'll see."

"I can't believe we agreed to travel with him," grumbled Amy, and then she and Rory made their shaking way down the halls of Tardis to join the Doctor in the central command room. The Doctor was clinging to the controls, laughing and howling in pleasure. "Doctor!"

"Ah, Amy, Rory!" the Doctor beamed, waving them down. "Come here, but be careful, I think something is on fire."

"What happened?" Rory called over the groaning and grinding of the Tardis.

"Well," the Doctor mused, pressing buttons as fast as he could. "We passed dangerously close to a white hole, and the electromagnetic radiation it was emitting overpowered the Tardis's circuitry. We're in a bit of a free fall right now."

"We're crashing?" Amy moaned, thinking this was something that happened more often than she liked with the Doctor. "We're crashing into a white hole?"

"Not _crashing_," the Doctor said. "I tried to stabilize the Tardis, jumping into the Time Vortex, and maybe a few galaxies over, but we swung a little too close to Earth."

"Which means," Amy said, rolling her eyes.

"Well, with the power cells low, the Tardis couldn't counteract the gravity pull, and we're being pulled in-hence the free fall."

"So," Amy said, stumbling over and lowering herself to the Doctor's face. "What you're saying is, we're in free fall, heading for Earth's surface, with no way to break the pull of gravity?"

The Doctor ran Amy's words through his head and then nodded, still smiling. "Yes, that sounds right."

"Now, what part of that explanation was _not crashing_?" Amy asked.

"Well, you didn't actually say crashing," the Doctor pointed out, and then the Tardis gave a powerful lurch and all three were thrown to the floor. "Perhaps we should all hold on?"

Amy looked like she wanted to scream, but the Doctor just rolled away and let the rocking motion toss him around. Rory latched on to the control panel of the Tardis and then reached out and pulled Amy up to him. She settled down next to her husband to wait out the violent motions of the Tardis, listening to the Doctor laugh the Tardis scream. They started shaking more and more, and Amy heard the Doctor scream something about the Earth's atmosphere. The Tardis rolled and Amy thought she was going to be sick, when suddenly, one of the levers shot forward and the Tardis's Time Rotor came to life. Amy watched the green light flash against the walls, and she felt the Tardis slow bit by bit. Though the Tardis was slowing, the ride wasn't nearly over. The sound of whistling wind was all around them and the doors to the Tardis shook harder and harder.

"I think we're landing!" cried the Doctor, and the Tardis was thrown forward one last time, grinding to a gritty halt. The Doctor, lying on his back, released a pent up breath in form a whoop of joy. "We're here!"

"_Here_!" Amy snarled, struggling to find her footing, but found that the Doctor, was already at the door. "Where exactly is here?"

"No clue!" yelled the Doctor, and vanished out the door of the Tardis.


	2. Second Chance

Second Chance

_Right, Physics! Physics, eh? Physics, physics, physics, physics, physics, physics. Physics! Hope you're getting all this down._

_-The Doctor_

"Who is that?" Clary asked Jace under her breath as they settled into their seats for calculus. "What happened to Mr. Moran?"

Jace, who was organizing his notes from the last lesson, hadn't been paying much attention to the strange man standing at the front of the class, but Clary's interest in him caught his attention. "He reminds me of a neurotic puppy," Jace dismissed, but Clary was still staring at him intently. "You can't tell me you think he's cute."

Clary flushed. "I didn't say that," she murmured, looking down at her hands. "Though I do like the British accent. I was just wondering what happened to Mr. Moran. He said he would check over my exam corrections with me."

"I'll go over them with you," offered Jace.

"I think it'll be better if I have the teacher do it," Clary said, taking the measure of the man before her. He was young, younger than Clary thought a teacher could be, and his face was set in a perpetual smile. She watched his eyes jump from student to student, to the board at the front of the class, to the work book before him; he looked very friendly. "I'll talk to him after class."

"He's wearing a bowtie," Jace said in mute horror, as if Clary hadn't spoken. "A bright red bowtie."

"Jace!" Clary giggled, but quieted as the man called the class to order.

"Hello, class," the teacher said, jumping up and fussing with his bowtie nervously. "Mr. Moran has been called away on family business; I'm Mr. Smith, and I'll be your new calculus teacher."

After the first twenty minutes of class, the students decided, as a collective, that Mr. Smith was the most eccentric teacher they had even encountered. He was passionate about math in a way Mr. Moran hadn't been, and would often lose track of the lesson, going on about things like quantum mechanics and recreational mathematics, writing across the board so quickly even the most astute of the children asked him to stop. During their first set of work problems, he jumped from place to place, offering help when asked, but mostly posing more confusing questions to the students. A few grumbled under their breath when he walked away. When he approached Jace and Clary, he gave a pause.

"You two," he said suddenly, stepping up and running his eyes all over their faces. "What are you two doing here?"

Clary's mouth dropped in terror and her eyes inconspicuously scanned her arms; if she had left stray runes in the open, her father would beat her. Jace, however, was quicker on the draw, and he raised an eyebrow. "We're in your class, Mr. Smith. I'm Jace Lightwood and this is Clarissa Morgenstern."

Mr. Smith shook his head. "I know you're on the list, I saw your names, but," and here, he lowered himself down to their desks and dropped his voice, "what are you doing in _here_?"

"Learning math," Clary squeaked.

They watched Mr. Smith's eyes widen, his thoughts drifting far away and his mouth open in a charming, confusing expression, but then he blinked and composed himself into the image of a very serious man. He nodded saying, "Well, yes, of course. I meant…well, what are you doing in this corner? The lighting is completely wrong for math, you'll ruin your eyes that way." He pointed to the front of the class where there were two spare desks. "Go on, move up there."

Jace and Clary exchanged nervous looks and then picked up their things and moved to the front of the class. Mr. Smith watched them, his face blank but his mind processing information in overdrive. Clary dared a glance over her shoulder at Mr. Smith, and he offered her one of his big smiles and then moved on to the rest of the class. For the rest of the hour, Jace and Clary sat hunched over their new seats, trying to work their way through calculus. At the end of class, Mr. Smith asked different students to come up to the board and work through their calculations. The last one, he called Jace forward, and as he turned his back on Mr. Smith, Jace felt the hairs on the back of neck tingle uncomfortably. However, when he turned back to Mr. Smith, the young man was smiling like a mindless Mundane.

"Very well done, Jace," Mr. Smith said as the bell rang, signaling the end of class. "You're homework tonight is to read chapter four on differential trigonometric functions and do the first five practice problems. I'll be collecting them tomorrow at the door."

Jace returned to his seat, gathering his books and then taking Clary's as well, but Clary hung back. "Jace, you know I have to go over my exam corrections, or Father will be furious with me," she whispered under her breath. "I'll only be a few minutes."

"I don't like it," Jace said back, putting her books back down. "I'll meet you in English, but if you're not there in fifteen minutes, I'm coming back for you."

Clary sighed, but she had accepted a while ago that Jace was overprotective where she was concerned. "Alright, just fifteen minutes. I'll be fine, Mr. Smith seems really nice."

"Nice, but weird," Jace growled, shooting the young man another look before he turned and left Clary alone.

"Mr. Smith," Clary said anxiously as she approached his desk. He glanced up at her and she saw that paper he'd been studying. There were calculations the likes of which she had never seen, numbers and symbols that didn't make any sense. She wondered where Mr. Smith had learned it. "I-our class took an exam last week, and Mr. Moran said if I went over my exam and did the corrections he'd sign it, and give me some points back…" she warbled off as Mr. Smith's green eyes widened in surprise. "Will you look over my corrections?"

Mr. Smith shrugged and held out his hand for the corrections. "Why not? Let's see what you've got here."

Clary stood nervously, watching the clock tick the minutes while Mr. Smith's eyes darted over the paper, his long fingers following her work through. She noted, impressed, that Mr. Smith didn't use a calculator of any kind to convert or check her answers, just mumbled under his breath. He leaned back, pushing the paper toward her, and Clary realized it had taken him only three minutes to check eleven problems.

"Why don't you sit down and we'll go over the work," offered Mr. Smith.

"I have class right now," Clary said, looking again at the clock.

"I'll write you a note," Mr. Smith replied simply. "Come on, sit down. Do you want a jammy dodger?" Mr. Smith reached beneath his desk and pulled up a small tin full of them. Clary stomach lurched in hunger.

"I'm not hungry," she said at the same time her stomach growled, but the burning of the five welts on her back, reminded her what would happen if she ate again.

Mr. Smith raised an eyebrow. "Really?" But Clary just shook her head, so he took one, and put the rest away. "So, your work is all right, a little messy, but all right. There's a few tricks I can show you, dealing with the differentials if you'd like; it'd be really useful for the upcoming exams and physics. Would you like to learn?"

"I-I don't really have the time right now," Clary mumbled, thinking how absent-minded he was.

"Well, of course, but after school or something. I'll probably be offering some review sessions here for all the students-including your friend Jace." Mr. Smith smiled proudly, as though because he knew they were dating, he'd noticed something really brilliant. "Not today of course, after out next quiz to let the students see where they're at. Would you be interested in something like that?"

Clary knew her father would never let her and Jace stay after school. When he gave them a time, they met that time. "I'm busy after school."

"Tutoring?" Mr. Smith said next. "You can get a tutor. I can tutor. Haven't done it in a long time though. Something to think about for now." He said all this very fast, and Clary found herself nodding.

"But, all the corrections were right?" she pressed, trying to return his attention to her work and the credit. "I've done everything right?"

"What?" Mr. Smith asked. "Oh, yes, yes, this is all correct. Let's see, eleven problems, I'll give you six points back. Sound fair?"

Clary felt her heart almost burst. Mr. Moran had offered her four points, at most, if everything was right. Mr. Smith had just raised her grade on the exam to an A-. "Thank you," Clary said breathlessly. "And I'll speak with my father about the tutoring." She gathered up her books while Mr. Smith added the points to her score and signed it.

"This will serve as your pass to class, right?" Mr. Smith asked as he stood up to show her out of class.

"Yes, and thank you again," Clary said, meeting his eyes quickly. She was startled by the light that seemed to be radiating out of them. She knew he was smart, but that was more than books and studying in his eyes.

"Not at all, Clary; you know, you're not bad at calculus just because you got a B on one exam. That's a perfectly acceptable grade." He glanced up and down Clary's nervous figure, and sensed her discomfort.

"I know," she sighed, and then tucked the test into her binder and left.

When she arrived at English, Jace was holding a seat for her. Mr. Arnold, her teacher, glanced at the test and the signature, but didn't press her too much. Clary was an excellent student, quiet, respectful, well-read; he never had trouble from her. Jace watched Clary like a hawk as she crossed the room and joined him at their table. The other two girls who were sitting with Jace glared when she sat down.

"What are we doing?" she asked under her breath.

"Questions on the board." Jace indicated the list of questions, and then curled his lip at them. "I'll never understand Shelley."

Clary pulled out her copy of _The Modern Prometheus_ and flicked through the pages, finding the lines she wanted. She understood how confusing Jace must have found the novel, since it had nothing to do with demons, demon slaying, demon hunting, demon anything, and he had spent his life reading only that, he would find anything else boring. "No, you wouldn't, would you?"

Jace scowled delightfully and the two girls sharing their table giggled as if he'd said something. "How was Mr. Smith?"

"He gave me six points back, and offered to tutor me if I needed help," said Clary.

Jace raised an eyebrow. "Six points is an A-."

"I know," Clary said, seeing the girls across from her looking at her in disgust. They clearly didn't see how important a calculus exam was. "Do you think Valentine will care if I tell him-"

"Mr. Lightwood," said the teacher, "Would you care to share with the rest of the class what you and Ms. Morgenstern are discussing?"

"I find Shelley's concept of reanimation dull, and Clary is far more interesting," Jace said smoothly.

The class laughed and Clary blushed; Mr. Arnold rolled his eyes. "I'm afraid I disagree, and, since, you seem so eager to speak, you can read for us. Chapter five, if you please."

Jace sighed, but knew there was very little he could say or do otherwise. The school was one of those private college-preparatory schools were even a whiff of trouble was reported to the parents; Jace suspected it was part of the reason Valentine sent them there. He cleared his throat and read, "'It was on a weary night in November that I beheld the accomplishment of my toils…'"

When the final bell rang, signaling the end of classes, Jace and Clary collected their English papers. It was ray of hope for Clary, as she had gotten a 97% on it, and had no reason to fear her father's wrath. Jace, slightly below her, at 95% grumbled about favoritism, but didn't complain. It didn't make much difference for him since he wasn't eating for three days anyway. They made their way down the halls and a set of stairs to where their lockers were before donning coats and going to wait on the steps of the school for Jonathan or Valentine to collect them.

Outside, it was cold and the sky was clouded over, preparing for rain. Clary huddled close to Jace and, without thinking, he opened his arms and drew Clary against his side. There were a few other students milling about, and a few of the girls were smiling over at Jace, ignoring Clary completely, but he offered them a blank, uninterested look, and stared contemplatively out at the street before them.

"There's something I can't place about Mr. Smith," he said in an undertone. "He's not…right, somehow. Could you feel it when you were around him?" Clary thought back to the time she'd spent around Mr. Smith; she hadn't noticed anything strange and told Jace as much. He rubbed his arms. "No, Clary, I'm sure. I just don't know what he is."

"Well, what could he be? I mean, there are no demons, and the Downworlders are in hiding-the ones that are left." Clary let the end of her sentence hang, but then pushed on quickly before she had to consider the implications. "He's got to be human."

"Logic says yes," Jace muttered, "but I just _feel _wrong."

Clary knew how disconcerting it was for Jace to know he was wrong about something so internal. He had spent his life hunting down creatures, trusting his senses to lead him to the target, and now, life was smacking him in the face. She rubbed his hands. "It's okay to be wrong."

"Don't let Valentine hear you saying that," said Jace darkly, and then relaxed against Clary. "Do you know whose coming to get us?"

"If it's Jonathan he'll let us sit in the rain," grumbled Clary. "If it's Valentine, I think we're in trouble."

Jace and Clary watched a few more cars pass by when one that was vaguely familiar pulled alongside the curb. Clary started when she recognized the inconspicuous, black Lincoln. Her father _never _let them ride in the car. When the door opened, Clary realized why the car had arrived and not Valentine. Jocelyn, looking stunning in dark jeans and a fitted sweater, emerged from the driver's seat, waving at them.

Clary groaned inwardly. _Why don't you just stay at home? Why can't you just leave me alone?_

"Smile, Clary," Jace ordered in her ear, and then pulled her to her feet.

It was hard for Clary to smile at her mother, when, in reality, her mother wasn't there. She'd watched Valentine mark Jocelyn, watched her mother's eyes glaze over and then fall back into place, a pleasant smile with it. He'd done something to her, Clary knew, done something that made her blind to the truth. It was like she saw the world through a window, tinted with Valentine's love. Jocelyn knew that Valentine beat Clary and Jace, but somewhere there was a disconnect, and she thought that it was for Clary's own good. Jocelyn was in love with Valentine and it made her a mindless mother figure, who occasionally sank down to Clary's world to offer her the comfort of a touch or kind word, but never the protection Clary was begging for.

"Clarissa," Jocelyn said, pulling Clary into her arms for a hug. "And Jace. Look at you two, sitting out here in the cold. Come in, come in, we'll stop and get some coffee or tea on the way home. Something to keep us warm."

Clary followed her mom, head down, while Jace picked up both their book bags. When he looked up one last time at the school, he caught the unmistakable figure of Mr. Smith watching him from the second story.

* * *

The Doctor didn't waste any time hanging around his classroom once the halls were empty. He shot out past three of his fellow math teachers coming to investigate the new meat with nothing more than a wave and a shout. He was down the stairs, through the halls, and almost to the front doors when the principal hailed him. At first, the Doctor, unused to the name Mr. Smith, had kept going, but his brain caught up to his legs in a moment later.

"Yes, Mr. Smith. That's me!" he said, turning after, rubbing his hands together. "What do you have to say to Mr. Smith?"

The principal gave him a strange look. "I just wanted to know how your first day went."

"Oh, it went excellent, just dandy; you've got an excellent school here, filled with…" the Doctor looked about him. "…students."

"Well, yes," said the principal. "I just wanted to make sure none of your classes gave you a hard time. You must realize how _young _you are to be teaching at such an advanced school."

_Advanced?_ thought the Doctor to himself. _When I was seventeen I wasn't learning calculus, that's for ten year olds. _His mind wandered off to the math he had learned when he was seventeen but then he smiled and said, "Everyone was welcoming as could be, now, if you would excuse me, I've got a nasty hand-break that needs fixing. Don't want to go wandering off into the Middle Ages or something."

The principal thought Mr. Smith must have misspoken and nodded. "Well, if you need help with your car, I know an excellent mechanic."

"Car?" the Doctor repeated, but then spun about on his heel and ran.

The Doctor hurried down the street and into the alley a few blocks over from the school where the Tardis had materialized. It really had been a prime location, in the middle of New York City, and right next to his new job, and, apparently, smack in the center of a nephilim quagmire. The Doctor paused outside the Tardis and ran his hand lovingly over the chipped paint on the door front. "Then again, you always get me somewhere interesting, don't you?" he said, and then threw the door open.

"We've got nephilim!" the Doctor announced the moment he'd closed the door.

Amy and Rory had been sitting on the stairs, wondering where they might have been right now had the Doctor not crashed them, when he arrived, and Amy glanced to Rory. "What, we've got a rodent infestation now or something?"

"Rodent?" the Doctor said, sounding disappointed the Ponds hadn't been more impressed by his statement. "It's not nice calling people rodents."

"Well I just assumed nephilim was a space rat or something," Amy shrugged. "Or a space virus."

"Or a space invasion," Rory added.

"Yeah, or that," Amy agreed. "You want to clarify?"

The Doctor had reached the screen on the Tardis and was typing into it. Amy and Rory joined him just as the screen came life and brought up the picture of a man with wings sprouting from his back. "Nephilim are alien human hybrids who showed up about two thousand years ago, right around the same time some inter-dimensional alien parasites arrived here. There's been a war going on since."

"Alien human hybrids?" Amy giggled, winking at Rory

"Yes, the aliens used gene manipulation to create a new race," explained the Doctor, missing Amy's sparkling eyes. "The nephilim, though mostly human, possess super human abilities, and utilize these markings," here, the Doctor pointed to an image of a rune on the screen, "to help them in battle. It's genius really, see, the stele they use to make the runes triggers certain hormone production, that lends to their superhuman abilities. Simple and effective."

Amy stared at the image on the screen. "Isn't that an angel?"

"What?" The Doctor gave her a long look. "Well, I guess if you want to call them that, you can. But, they're just aliens like me."

"Nothing is that surprising anymore," Amy said with a shrug and then traced the rune with her finger. "So, you're saying we've got them?"

"It's rather odd," mused the Doctor, going to his seat and flopping down in it. "Two shadowhunter children in my classroom, learning calculus. I mean, that's not supposed to happen in the first place; they're supposed to be learning how to fight. Something is wrong…"

"Well, maybe their parents want them to learn proper stuff too?" offered Rory. "It can't be a very fulfilling life when all you learn is how to kill."

"It's not," agreed the Doctor, "but it still doesn't explain what they were doing there. Besides, what year is it?"

Amy glanced at the screen. "2007."

"That sticks out for some reason," hummed the Doctor, resting his chin on his hands. "Something important happened that year, I just don't know what." He remained seated for a few minutes then jumped back up and began scrolling through the file on nephilim faster than Amy or Rory could read. He gave a shout of victory and pointed very suddenly to the image of a man. Amy thought he looked rather imposing, tall and broad-shouldered, with white blond hair and grey eyes. She couldn't tell if she liked him or not. "This is Valentine Morgenstern, and in 2007 he raised an army of demons, those inter-dimensional parasites I mentioned earlier, summoned by the power of the Mortal Instruments, and tried to summon an angel to him to enslave the nephilim race."

"Enslave them?" Amy defiantly didn't like the man. "What happened?"

"What are the Mortal Instruments?" asked Rory at the same time.

"Mortal Instruments were three weapons sent by the angels to be used in time of dire need. They're a bit out of date if you ask me, seeing as I can accomplish much the same thing with a cell phone as Valentine could with all three."

"It's a cell phone?" Rory laughed.

"Sorta," said the Doctor. "He can use them to contact an angel. Anyway, he tried to commit mass genocide of Downworlders and enslave the shadowhunters, but his daughter," and here, the Doctor pulled up an image of young, red-haired girl, "and his stepson," and again, the Doctor showed an image of a handsome blond boy, "managed to thwart his plans, and then the two went on to save the world again when Jonathan, Valentine's son, poisoned by Lilith, tried to take over the world."

"So, where's the problem?" asked Amy, not having followed the Doctor's logic, but liking the look of the little red-head.

"The problem, Amelia Pond, is that those two children were sitting in my math class today!" the Doctor cried, finally putting the faces to the names of the children in his class. "Something is wrong. The Tardis didn't bring us here by mistake; something is wrong with the flow time."

"Again?" Rory whispered to Amy.

* * *

"Clary, your father wants to see you in his office," Jocelyn said as she settled on the couch in front of the television with her hot chocolate. "Jace, you too. I'm making dinner and it'll be ready at six. It's going to be delicious, something big before I head back to Alicante."

Clary, who was hanging up her coat, froze. _How could I have forgotten that? _she asked herself. Since Valentine's victory, he has split his time between New York City and Alicante, travelling between the two almost every day. Jonathan would often follow his father, coming back to the pent house in New York at night. Jocelyn, who loved both cities, would spend a week or two in New York, and then spend a month in Alicante. Though Jocelyn didn't seem too concerned with Valentine's treatment of Clary and Jace, her presence, at least, calmed his temper to a certain degree. With her gone, she and Jace would have to tread carefully.

"How long will you be gone?" Clary asked calmly.

"Oh, I'm not sure," mused Jocelyn. "I'd like to stay for three weeks maybe, and catch up with a few friends, and see to the new Clave. Would you like me to bring you anything back?"

Clary felt her heart sink. Her father never let her or Jace travel, and had made it very clear that until they were willing to submit to his whims, they would be staying locked up tight in New York. Jace hadn't taken it well. "Could I have some new books, maybe?" asked Clary, shooting Jace a look.

"Of course," Jocelyn said, turning to Jace. "And you, Jace, can I get you anything?"

It was the only thing Clary still liked about her mother, that she seemed to genuinely love Jace. She had been one of the driving forces behind Jace's placement in their home; pleading with Valentine about how much Clary loved Jace, how she and Valentine had been the same age when they fell in love. Clary knew the reason she got to sleep beside Jace at night was because of her, and for that, she was grateful.

Jace seemed to know it too. "No, I'm fine here." But Jocelyn gave him a long, knowing smile, and he pulled childish grin. "There's a cake shop I'm rather fond of, and they make a great chocolate and caramel cake."

"It'll be perfect," Jocelyn said. "We'll have a party when I come back. Now, why don't you two run off while I get dinner going? Have you seen Jonathan?"

"He's still in Idris," Clary tossed over her shoulder as she and Jace climbed the stairs up to Valentine's study.

Jace knocked, drawing Clary against him, and waited for Valentine to call them in. When they entered, they found Valentine seated behind his desk, running over documents from the Clave. As they drew level to his desk, Valentine looked up. "And what have you two brought me?"

Clary was shaking against his side, so Jace spoke first. "My English paper."

Valentine snapped it up, eyes scanning it and rested on the grade. "You're cutting it rather close, aren't you? Clarissa, I take it you're not going to disappoint me again?" Clary sighed, presenting the essay, and fingering the math exam. "Well, done, Clarissa. You may join us for dinner tonight."

"Thank you," Clary bit out, and then pulled out the old math exam. She watched her father's eyes darken, but still gave him the test and corrections anyway. "I spoke with my math teacher, and he agreed to give me six points back on the exam; my grade is an A- now."

As his eyes flicked over the exam, Valentine seemed unimpressed. "I thought Mr. Moran was only going to give you four points?"

"We have a new teacher," Jace answered. "His name is Mr. Smith."

Valentine slammed the exam down making both Clary and Jace jump back, but his voice, when he spoke, was tempered. "This Mr. Smith is an idiot; clearly, he doesn't understand how the real world works." Valentine stood and directed both Jace and Clary around to his side of the desk. "Do you think it's fair to give points back if you redo the work?" he asked them.

Again, Jace spoke, sensing Clary's fear. "If they're earned, I don't see why not."

"You believe in second chances?" pressed Valentine.

Both Jace and Clary knew this was going somewhere neither of them wanted to be. "I think some people deserve them," Clary whispered.

"Of course you do, Clarissa, because you were raised to think it's okay. You were raised with the idea that failure is an option." Valentine jerked Clary from Jace grasp and forced her to grip the edge of the desk, her little fingers resting on the wood, out in the open. "In life, as Mr. Smith clearly doesn't understand, there are no second chances, no do-overs; if you make a mistake, you're dead, and then what?"

"I don't know," Clary whispered, watching as Valentine went to one of the book shelves and retrieved a heavy, leather bound book. Jace moved suddenly, blocking Valentine's way.

"Leave her alone, Valentine," he said, brushing his hand against her in a comforting gesture. "She was only trying to make you happy."

"She's a fool, and if you don't move, you'll share in her punishment," he warned simply.

"I'd gladly take all of it," Jace answered swiftly.

"Jace," Clary moaned.

Valentine reached out and pulled Jace aside, whispering in his ear, "You're going to owe a lot more than a beating for that. I trained you once to obey orders, now you're making me do it again."

Clary watched Valentine shove Jace onto the floor and approach her. "Don't hurt him," Clary pleaded.

"I'm afraid dissention among ranks is punished in the most extreme form it can take," Valentine shrugged. "Now, bite down on this pencil. I don't want your mother hearing you screaming."

Clary swallowed back any pleading and opened her mouth so Valentine could place the pencil there. She bit down carefully, arranging her tongue so she wouldn't touch it, and then waited for Valentine to begin. It hurt much more than she expected; and Clary was scared her fingers might break. As he brought the book down again and again on her fingers, Clary whined, but never screamed. She saw bruises forming, red welts, and finally, heard a crack. Valentine must have heard it too, because he paused and examined her fingers closely before bringing the book down once more on the broken one.

"You can go help your mother now," Valentine said, turning away from her and back to Jace who was still kneeling on the floor. Clary pulled her hands back and stared at the battered, twisted fingers; her eyes found Jace and she saw the look of raw pain in his eyes.

She stumbled over to him on the floor and wrapped her arms around him. "I'm sorry I got you in trouble," she sobbed. "I'm so sorry; I'll make it up to you tonight. I'll steal you food, I'll write your English homework. I'll let you copy math…"

"Clary just go." Jace cupped her face in his hands and kissed her. "Just go help your mom, don't worry about me, I'll see you after dinner." Clary wanted to stay, but she saw the shadow of her father cross her, and Jace pushed her away. When she lingered at the door to the study, she saw Valentine life an electrum wire whip.


	3. The Girl Who Waited

The Girl Who Waited

_So, is this how it works Doctor? You never interfere with the affairs of other peoples or planets, unless there are children crying?_

_-Amy Pond_

"May I please be excused to do my homework?" Clary asked, her eyes down on the empty plate before her. She thought if she ate any more she might be sick, and her mother had promised them fudge ice cream; Clary didn't think Valentine would like it if his daughter threw up all over the place. "I have a lot of calculus left."

"I bet," snickered Jonathan, who had only recently returned home.

"Yes," Jocelyn said, "but I'll leave you some ice cream as a snack in the freezer for later tonight."

"Thank you," Clary murmured and then picked up her plate carefully, aware of her broken fingers, and fled.

Family dinners had become a special form of torture for Clary. She could have accepted sitting across from her brother, and having her father's cold eyes on her, but it was her mother that drove home the spike. She was completely blind to Clary's predicament, and though Clary would sit beside her, meeting her eyes, trying to jog some maternal instinct, Jocelyn remained blank. Valentine knew exactly how horrible Clary felt, how much she wanted her mother back, and he knew how much it hurt her to feel Jocelyn's absence.

When Clary arrived at her room, Jace was seated at the desk, scribbling homework problems. There were many sheets on the ground and Clary felt apprehensive. "Is it that bad?"

Jace jumped when Clary spoke, but then smiled warmly at the sight of her. "I won't lie, I don't know what I'm doing. I've tried everything, but I don't know how to solve these, and they're due tomorrow, first thing…"

"Maybe we can go in early and ask for help?" Clary offered, joining Jace and staring at the many calculations. "We can skip lunch, since you can't eat anyway, and see if Mr. Smith will help us."

"Why would he assign them and then give us the answers?" Jace asked, and then tossed his pencil. "I'm never going to understand Mundane school."

"It's not about how correct you are the first time around," Clary explained, picking up the pencil and kissing Jace's cheek. "It's about the learning process."

"Ridiculous," Jace muttered, and twisted to kiss her back, but his back suffered a sudden spasm.

"Is it that bad?" Clary asked, reaching for the hem of Jace's shirt, and he tried to pull away. "Jace, let me see it. I'll get the first aid kit and clean it up."

"I don't think it's going to help much…"

Clary managed to pull Jace's shirt up, and she wished she'd left it down. Like her, Valentine had only whipped him five times, but an electrum wire was much more biting than a leather belt. Where Valentine had hit him, ugly purple weal's had formed, and had left skin synching together under the intense temperature. Clary's finger traced the marks, drifting over the burst blood-vessels. She swallowed back her cry for his pain; Jace was right, there was nothing she could do with the first aid kit. While the whip had torn his flesh, the heat had cauterized it, closing the wounds at the same time.

"Tell me what you need, I'll get it for you," Clary said softly. "I'll bring ice or water, I don't care if my father catches me. Pain killers?"

"No, Clary, just don't let me roll over tonight, alright?" Jace asked, and then gathered up the math and gestured to the bed. "There's more room over there for the two of us to work."

For an hour, the two worked, and like Jace said, the problems were more difficult than expected. Together, they finished two, but by then it was nine, and there was the reading for English class, the chemistry homework, and Jace's worst subject of all, United States History. Clary, who had always been quick in history, offered to read aloud from _Frankenstein _while Jace completed a worksheet. It was Jonathan who broke their companionable work.

"So, is this what shadowhunters do nowadays?" sneered Jonathan. He strolled in, picked up the history book Jace was reading, and then tossed it across the room, so it slid out the door. "Father has sent me up to tell you, you're not to leave this room the rest of night, since he and mother are going out. He said he'll know if you left."

Clary and Jace didn't doubt that. There were a number of permanent runes Valentine has recently administered to them, one of them, he mentioned, was a tracking rune. "We're just going to stay in here all night?" Clary asked.

Jonathan shrugged. "Do your homework; Father sent this up for you." He offered Clary a large copy of the Book of the Grey and she looked at it warily. "He says you're to practice some runes you've been working on lately. Have a page of perfectly written runes ready for him tomorrow."

"He couldn't come up here and say this all himself?" Jace asked, snatching the book away from Jonathan.

Jonathan winked at Clary. "He's busy. Besides, I wanted to see little Angel Boy for myself. Show me these whip lashes."

Jace pulled himself away from Jonathan, his face curled in a snarl of disgust. "Keep away, demon boy."

Jonathan lunged with speed even Jace couldn't challenge, and caught Jace's wrist and clung to it tightly. "Come, little brother, show me the lashes. It won't be as bad as you think. I just want a peek, a glimpse. It'll make me smile."

Jace struggled and Clary jumped up. "Get out of here, Jonathan!" she ordered. "Go back to Idris, go away."

"Little sister, I'll deal with you as well if you're not careful. Jace, show me your back!" Jonathan jerked Jace forward and Clary shot after him like a feral cat. She jumped at her brother, and if she'd had claws, she would have scratched his eyes out.

"Clary, stop!" Jace ordered, seeing the dark turn in Jonathan's eyes. "Get back in bed. Go do your homework."

"No," Jonathan said in a low voice, "if Clary wants to play too, we'll let her join our game. Come, little sister, come and play with Jace and I."

"Clary, go back to bed," Jace ordered firmly, but then Jonathan jerked the collar of his shirt, cutting him off.

"You want to play, Clary?" Clary, who had been tossed aside in the struggle looked up through her messy hair.

"What do you want?"

"If you play with me, I'll leave Jace alone," Jonathan offered, tightening his grip on Jace as he spoke. "Come on, Clary, what's the worst that could possibly happen? You're my sister, I would never _purposefully_ harm you."

Clary neared her brother, and her senses were reeling, her mind screaming at her to run away from him, run away from the demon, but her heart was telling her again and again that Jace was in far more danger of Jonathan than her. Carefully, she put herself in reach of her brother and waited, heart pounding.

"You're such a good girl," Jonathan said sweetly, and then shoved Jace with enough force into the bed to topple him over the other side. By the time Jace had gotten back up to his feet, Jonathan was holding Clary, one hand clutching Clary's wrist, the other, caressing her throat. "Careful, Angel Boy, or I might just break your little play thing." He felt Clary's pulse jump and he laughed.

"You said you wouldn't harm her," Jace hissed.

"No I said I wouldn't purposefully harm her, and as far as I'm concerned, this isn't harming her," Jonathan said with an angelic smile. His hand, resting on her throat slid down her shoulder, pushing the sleeve down to reveal her pale skin. His hand vanished and returned with a small, sharp knife, which he toyed with before Clary's face. "It's good for her to bleed a little, it'll toughen her up. Just like father did to you."

"Just stop," Jace said desperately.

Jonathan chuckled, and slid the knife down, positioning it right over Clary's chest. "I could start here, you'd like that, wouldn't you, Jace? A little bit of skin, a treat; it must kill you to sleep beside her every night and know you can't touch her."

"What's wrong with you?" Jace demanded just as Jonathan began cutting Clary's shirt. "She's your sister!"

"This is for you," Jonathan cooed, slicing just a bit further. Clary, who could feel the cold kiss of the knife on her skin, barely breathed, but she was terrified Jace was going to overreact.

"Jace, don't, it's just a game. He's just playing with us! He's playing us off each other," she said urgently.

Jonathan's face turned an ugly color and he suddenly brought the knife down, cutting into Clary's skin. She screamed and Jace darted forward for her. With a grunt, Jonathan shoved Clary into Jace's arm, watching her clutch her bleeding chest. "Just a game, is it, little sister? Do you like how I play?"

Jace was holding Clary in the circle of his arms, and it was the only thing stopping him from lunging at Jonathan. "Don't you have some poor, defenseless animal to maim?"

"I'm doing just that," answered Jonathan with a sneer. "But you're right, Jace, I actually have a life to live. I think I'll go out tonight, maybe to a club, maybe bring someone home. I've never been one for the Mundanes, but they're so disposable, after all." He turned, looking over his shoulder at his bleeding his sister and a furious Jace. "But don't worry, big brother I'll make sure you're both tucked in tonight."

Clary, who was curled in Jace's arms shuddering, watched Jonathan go and collapsed onto the bed. "You're book is in the hall," Clary said weakly. "You can't study history tonight without it."

"I'm not worried about history," Jace said, eyeing the cut that was dribbling blood down Clary's front. "Let's clean that out and then I'll help you with the runes. We can go to bed after. I don't want to be up when Jonathan comes home with his guest."

* * *

Clary woke up early the next morning, to the sound of a woman laughing, and she knew that Jonathan's guest was leaving. Curious, she slipped from bed and crept out of her room, to the edge of the stair to catch a glimpse of the woman who would consent to a night with her brother. She watched as two figures came into view, one of them, her brother, his hair delightfully messy and his shirt loose and unbuttoned; the woman was tall and thin with a fall of chocolate hair that framed a very elegant face. She was beautiful and Clary didn't understand what such a lovely woman was doing with her brother. She heard them talking in low voices, and then the woman kissed Jonathan on the cheek as he showed her out.

When the door closed Clary waited on baited breath for Jonathan's return. He rounded the corner and caught her, but a small smile curved his face. "Jealous?"

"That you can go out?" Clary challenged.

"That Michelle spent the night with me," Jonathan returned, and watched Clary's face color in indignation. "Next time, when I tell you to stay in your room, stay there until I come and get you."

"Where are mom and dad?"

"Out," was all Jonathan said. "I'm the one seeing you and Jace to school today, so you might just want to behave yourselves."

Clary and Jace showered and dressed quickly, a little concerned about Jonathan being their escort, but he seemed in a good mood, only making sneering comments at Jace and ugly glares at Clary. When they arrived at their school, Jonathan glanced about at all the other students, and he rolled his eyes in a show of disgust. He didn't think much of the school and its teachings. He ushered Clary and Jace to the side for a quick talk.

"I don't think Father will be back from Idris, so I'll be here to get you when school ends," Jonathan said, eyes glittering. "I'm not free on time, so if you're late, they'll be hell to pay. Don't make me have to hurt you."

"Yes, I plan my day around that," Jace snapped back, shifting his and Clary's books around. "Really, I stay up late at night, thinking of ways to make _your_ life that much more troublesome."

"I always knew you dreamed of me," Jonathan replied with equal verve and then took Clary's wrist in his iron grip. "Clarissa, since you're the only Morgenstern about, I'll be trusting you to keep the brat in line, and, if you don't, you'll be the one to pay the price."

"People can see," Clary hissed as Jonathan twisted a little. "Jonathan, someone will see!"

"Those Mundanes can't see anything-"

"Excuse me!" someone cried, knocking into Jonathan completely by accident. Jonathan stumbled back, snarling under his breath, and Jace caught Clary deftly.

"Mr. Smith," Jace said quickly, arranging his features into one of surprised concern. He righted Clary and then reached out to help Mr. Smith in back onto his feet as well.

"Oh, good morning," Mr. Smith said brightly, running his hand through his hair and brushing off his tweed coat. "I must not have seen you there; I'm a little late for class. Who's this?" Mr. Smith had noticed Jonathan, standing to the side and staring daggers at the man who had broken his contact with Clary.

"This is my brother, Jonathan," Clary said weakly, tucking her wrist out of sight. "He was just dropping me and Jace off. He doesn't go to school here."

"Ah, right, right," Mr. Smith said, holding out his hand to shake Jonathan's. "I'm Mr. Smith, the new calculus teacher here and I completely forgot that I had class this morning."

"It's Tuesday," Jonathan pointed out unhelpfully as he shook his hand.

Mr. Smith waved his hand as if that meant nothing to him. "Tuesdays never count anyway, never had anything interesting happen to me on a Tuesday. In fact in the grand scheme of things, Tuesdays are just one of the those days that don't really matter." He was speaking fast again, something Clary found slightly adorable, and she saw Jonathan's face turn up into something charming, the anger and darkness fading quickly.

"It's a pleasure to meet you," he said swiftly. "I hear my sister isn't quite up to scratch on calculus, I hope she's not causing any problems."

Mr. Smith laughed as if Jonathan were being ridiculous. "Clary? She's marvelous! Calculus is rather tricky, especially the way it's taught here. I mean, when children don't learn anything about sequential mathematics until college, there's only so much you can do in calculus."

Jonathan's eyes had grown wider and he seemed slightly confused by Mr. Smith's sudden outburst. "Well, perhaps with you teaching her that might change."

"I do my best," Mr. Smith said with a smile. "Well, I must be off, and I suppose you two must have class. I'll see you in forth block-"

"Wait," Clary said suddenly. "Do you mind if Jace and I come and speak with you during lunch. We had some trouble with a few of the problems…" Clary could feel Jonathan's eyes on her, and she focused on Mr. Smith's kind, open face.

"Well, of course," he said with a bright smile. "Yes, yes, that would excellent. In fact, why don't you come with me and let me peek at the work right now. You too Mr. Lightwood."

Jonathan frowned just a little, watching his victims being pulled away by an overfriendly teacher. "I'll be here at three thirty sharp," Jonathan called, and made a point to pay Clary back for her escape.

"Now, let me see it," Mr. Smith said gently to Clary, and she offered him the paper. His eyes landed unerringly on the bruises forming on her wrist, and then darted to the mangles fingers. "What happened there?" he asked, turning his eyes to the math problems in front of him.

Clary tucked her wrist out of sight. "When you knocked into us Jonathan must have squeezed a little too hard," she said softly. "How is the math?"

"Oh, it's good so far, but I can see why you struggled," said Mr. Smith, handing her the paper back. His eyes went again to Clary's wrist but he made no comment.

"Thank you, Mr. Smith, we'll come back at lunch," Jace said, pulling Clary a little away.

"What about lunch?" Mr. Smith called as they went, but then made his way slowly to his classroom.

It was free period for him, so the Doctor settled at his desk, thinking back to Jace and Clary. "So, that's Jonathan," he mused, thinking of the half-demon boy. He seemed nice enough, though a little stilted, and probably thought he'd pulled one over the Doctor. "He wishes he could pull one over me." And then he set about to reviewing the math problems he'd assigned the children.

Jace and Clary sat through their first three periods with the same blank faces and disinterest. Some of the boys seemed interested in Clary, but Jace kept a very close watch on Clary, and anyone's eyes that drifted her way were met with angry glares. Of course, girls were in love with Jace, but he paid them no attention. When lunch came around Jace and Clary headed for Mr. Smith's room with their homework.

"Mr. Smith, can we come in?" Clary asked from the door.

He was running about, scribbling on the board, and whatever he was writing was not eleventh grade calculus. "What? Oh, yes, come in, come in. Sit down, we'll go fast since we only have lunch period." Jace and Clary smiled at each other. If Mr. Smith didn't consider himself fast to begin with, what was fast going to be? "Alright, let's get started."

Mr. Smith launched into an explanation of the mathematics, his hands moving across the boards, and his voice accompanying with equal speed. Jace scribbled as fast as he could, realizing that when Mr. Smith explained things, it made a little sense. Clary, who was still behind, kept falling behind. Mr. Smith turned about and saw Clary, and he smiled kindly down at her.

"Let me see," he said, and came up behind her, peering at her work. "Yes, it's a bit confusing when you don't understand the actual, physical implications of sinusoidal functions. However, for now, this will have to do."

The bell rang and the voices of students echoed down the halls. "Thank you, but I think I'll never understand it," Clary said with a sad smile.

"Well, my offer of tutoring is still on the table," said Mr. Smith. "It couldn't hurt, and I'm sure even Jace could benefit from the one on one time with me. Besides, haven't you started physics yet? I'm excellent when it comes to physics."

Jace titled his head, considering. "We would have to speak with Clary's father, but it would be very helpful."

"I'm more than happy to speak to your father," Mr. Smith said at once. "Next week is the mid-semester evaluations, and your parents will be coming for parent-teacher conferences. I'll mention it then, if you'd like. However, how about I write down my phone number for you, in case you want your father to speak to me sooner? Have him call me if you're interested." Mr. Smith scribbled down a number with more digits than Clary thought a number had. "Just call, I'll answer."

"Oh," Clary said suddenly, snatching up the paper with the number, "I'll take that. My father might be a little busy though, what with work."

"What does your father do?" Mr. Smith asked as the class filed in, an eyebrow raised in question.

Clary's face fell a little. "He-he is a manager of a company," she said uncertainly.

"Ah, of course," Mr. Smith said, nodding and motioning the students to their seats. "Have him call me, Clarissa."

"Have Valentine call Mr. Smith?" Jace snickered under his breath as they watched Mr. Smith write on the board. "I think if he could, Valentine would shake the life out of this man."

"After what he said last night? I think you could forget the shaking and just settle for the killing," said Clary and then set to copying Mr. Smith's notes.

When school ended later that day, Clary and Jace sat on the steps, anticipating Jonathan's return. They had made sure they were early, not wanting to give Jonathan any reason to punish them more, and found that they had nothing to do but watch happy students go home. As they waited, a woman crossed the street, headed for the school; Clary nudged Jace and pointed at the woman.

"She's pretty," Clary murmured, not really sure why she was drawn to the woman. "I hope I look like that when I'm older."

Jace chuckled and examined the woman. She was tall, willowy, with long red hair that hung in loose curls, and a warm round face. She was dressed a little oddly for New York, Jace thought, since she was in a short jean skirt, reddish shirt and a worn, brown coat, leggings and boots. As she approached the school, she looked at the name of it, but frowned; then she noticed Jace and Clary seated on the stairs and smiled uncertainly.

"Hey, this is a school, right?" the woman asked, and Jace at once detected the Scottish accent.

"Yes," Clary said. She drew level to them, and Clary saw she had soft brown eyes that were full of some sort of emotion Clary didn't recognize. "Were you looking for someone?"

"Well, actually, yes," she said, brushing some hair out of her eyes. "A teacher, the D-Mr. Smith. He's sorta young, tall, wears a bow tie, has amazing hair."

"You call that amazing?" Jace asked, but he was smiling. He also liked the woman. "He's our calculus teacher."

"Yep, that sounds like him," the woman said, rolling her eyes. "I'm a friend of his, Amy."

"His friend?" Again, Jace smiled.

"Yeah, my husband, Rory, and I live with him," Amy nodded. "It's kinda hard to explain, we travel around a lot, and every now and then pick up some odd jobs. So, you're students in his class, huh? What's that's like?"

Clary and Jace looked uncertainly at each other. "It's a little crazy," Clary admitted. "I mean, he's a great teacher, but he's _really_ smart, and he knows a lot…but I'm not good at math, anyway."

Amy shrugged. "Imagine living with him. I swear he stays up all night with his constant…_thinking_!" She burst into laughter and watched a nervous smile spread across Clary's face. "I couldn't imagine having him teach me math. I mean, I was horrible at math to begin with-used to copy off Rory in school-but having Smith teach you would have made my brain burst."

"He's really helpful, though," Clary added. "He offered to tutor me and Jace after school."

"That's nice," Amy agreed, and then gestured to the side walk. "You mind if I sit and wait with you. No point in me getting lost in that school. My high school had four hundred kids, max."

"Of course," Clary said, and she scooted over to make room for the nice woman. "You're not from around here, are you?"

"You've got a Scottish accent," Jace said at once. He prided himself on being able to identify accents, and hers was a giveaway anyway.

"I do," agreed Amy. "I'm from Scotland. I told you, we travel. New York is a long way, though." Something about what she said made her eyes glow.

"What brought you here?" Clary asked wonderingly.

Amy looked away, smiling a strange, knowing smile, very much like Mr. Smith. "It's kinda hard to explain, really. Sometimes, we know where we're going, and then other times it's a little random. We ended in New York a bit by accident, to tell the truth, and our transportation was a little out of shape, so we were going to hang around a few days, but…well, things came up."

"You got stuck long enough for Mr. Smith to look for a job?" Jace asked incredulously. "Is your car broken that bad?"

Amy thought of the Tardis, its glowing green lights and the lovely groaning noise, and how it always seemed to bring them to some place they were needed. "It's a little touchy."

Jace, who was a shadowhunter, didn't know the first thing about fixing a car, and Clary, who was a sixteen year old girl, wasn't well versed either. "Cars can be that way," Clary agreed. "Do you think you'll be around long?"

Again, Amy smiled oddly. "Oh, long enough. Mr. Smith likes to travel more than anyone I know, but when he finds a place that's just right, he'll stay a bit. I suppose we'll be in New York for a while."

"I don't think I could ever live like that," Clary murmured. "Moving from place to place with no way of knowing where you'll end up. It's too uncertain."

"You come to love it after a while," Amy said, her eyes full of memories. "Mr. Smith, he's seen the world, and when you travel with him, it's like you're seeing it all over again, through clearer eyes. Except, it's just that much better, because he's just wonderful, everyone thinks he's wonderful."

"I bet Rory loves hearing you say that," Jace chuckled, and Clary shoved him.

But Amy laughed and mussed Jace's hair playfully; Jace, who had never had an adult rustle his hair lovingly, jumped a little. "No, Rory loves Mr. Smith as much as me, though, he sometimes doesn't like to travel as much."

"What do you do when you don't travel?" Clary was interested in this woman, this strange, other-worldly woman, who seemed to love them like children.

"I'm a model," Amy said, blushing a little. "Rory is a nurse."

"It must be hard to find work," Jace mused. "How do you pay for all your travelling?"

"Oh, it's-it's sorta free," Amy shrugged. "Mr. Smith takes care of most of the traveling since he's really the only one who can drive the …car."

"You can't drive?"

"Well, only in Europe," Amy reasoned. "I'd drive on the wrong side of the road here, wouldn't I? It's just easier to let him manage that."

"That's very kind of him," Clary put in, wishing she had a friend like that. Really, she wished she had anybody who would care for her like that beside Jace.

"Well, who knows," Amy said airily. "Maybe one day you'll travel too. Maybe once you two graduate and figure out what you want to do, maybe you can travel with us too."

"Oh, I don't think I could ever go," Clary mumbled, thinking of her father's watchful eyes. "We've got plans for the future already."

"Really?" Amy was intrigued. "You're a little young to know your life, I didn't know who I was until I met Mr. Smith, I didn't figure out my job until I'd done a fair bit of running with him. What I'm saying is, don't let people tell you how to live. It's your life, and it's not for any other person to decide."

"Sometimes I like to think that," Clary said, and then saw Jonathan coming toward them. "My brother is here, Amy. We have to go."

"Your brother?" Amy looked about and saw the handsome young man coming toward them. She thought of the Doctor telling her about Jonathan being poisoned and wondered if he would hurt the children in public. "He looks pleasant."

"He's very protective," Clary said, catching the look on his face when he saw Amy beside them. He looked just as furious as he had when Mr. Smith had bumped into them.

"I always wondered what that was like," Amy mused. "Having siblings, I mean. I barely had parents." Then she laughed at some private joke. "At least he comes to get you, New York could be a dangerous place for two kids."

Jace bristled at being called a kid, but relaxed when Clary pinched him. "We're grateful."

Jonathan approached them, eyeing Amy closely. "Who is this?" he asked, not unkindly.

"I'm Amy," she said before Jace or Clary could speak. "I was just waiting around for Mr. Smith, I'm a friend of his."

"Ah," Jonathan said, and he waved Jace and Clary over. "He's a bit absent-minded, don't you think?"

Amy grinned. "He just does a lot of thinking."

"You call it that?" Jonathan asked, and his smile faltered a little when he felt the hairs on the back of his neck. It felt like something…_not human_ was about. It wasn't quite what a demon felt like, but it didn't feel human. "Well, we've got to go, we're having dinner with father this evening and he wants us ready by six."

Amy gave him a strange look but then winked at Clary. "I suppose I'll see you two about."


	4. Speak

Speak

_Shut up! I'm making deductions, it's very exciting._

_-The Doctor_

"I met Jace and Clary," Amy said, leaning back against one of the desks in the Doctor's classroom. She surveyed the room, eyes lighting on the posters on the wall of galaxies and paramecium, with proclamations like, _Math Is Universal _or _Math Is Life_ and shuddered, thinking of her own math classes back in high school. However, this room seemed ideal for the Doctor, who was writing out a complicated proof on the board. When he finished, he sniffed and crossed his arms. "They seemed very polite, a little nervous, though."

"Well, you were a random woman who came up and started talking to them," pointed out the Doctor. "Then again, Clary has some bad nervous ticks. Did you meet Jonathan?"

"That blond boy is supposed to be part demon?" Amy asked. "Don't get me wrong, the boy's got a bit of an attitude, but he's not evil."

"No, he's not," agreed the Doctor. "But he's been poisoned and it drives him a little mad. It's hard to explain exactly, but the poison affects the basil_ ganglia_ and adjacent parts." He said the word ganglia with an odd little shudder.

"I'm not a doctor," Amy hummed.

"The basil ganglia is the center that evolved the reward-punishment system, the part of your brain that drives your most basic instincts to survive." The Doctor smiled at Amy. "You humans and your brains."

"Hey, just because our brains haven't reached Time Lord level doesn't mean we're not brilliant in our own way!" Amy cut in.

"I didn't say that. Anyway, what makes the poison so affective is that the basil ganglia, while being the center for your distance cousins' instincts, evolved in humans, and is now the center for decision making." He looked very serious. "This can have devastating effects on the boy. He doesn't have the same inhibitions a normal human would have; he doesn't understand empathy or suffering. In effect, there is disconnect between Jonathan's actions, and his understanding of his actions."

Amy frowned. "If he doesn't understand what he is doing is wrong, is he guilty of anything?"

"As far as I'm concerned, no," the Doctor said firmly. "Jonathan clearly needs help, but will he get it among humans? I don't think so. However, whether he is guilty or not, he still poses a threat to anyone around him."

"That dangerous?" Amy wondered.

"Think of it like this," the Doctor began. "The basil ganglia was the center for instinct driven actions. The main instincts of all living things are to survive, which involves finding food, fighting off predators, and securing at least one mate to procreate with. If Jonathan has these instincts, but doesn't understand them, he could harm any number of people just to, oh, I don't know…get his favorite sandwich from the pub."

"That's a bit extreme," laughed Amy. "Anyway, have you figured out what to do with Jace and Clary? Rory and I were talking, and maybe we could pretend to be police or something, and show up at their door and snoop around?"

"No," the Doctor said at once. "I don't know why Valentine is alive still, but it doesn't make him any less dangerous. I'm trying to figure out exactly what happened, but until I get a better idea of the war and what happened and what obviously _didn't_, I don't want any snooping."

"We're never going to find out that way," Amy complained. "You can't just up and ask Jace and Clary why Valentine is alive."

The Doctor shrugged. "Right now, I've got no better alternative than to wait and see. Besides, next week is parent-teacher conference week, and I'm sure Valentine will be coming to see how his daughter is doing." Here, the Doctor smiled slyly. "I could slip a tracking device of some sort on him; listen in on his conversations."

"That's rather sneaky of you, Doctor," Amy said, and jumped off the desk. "Let's get out of here. Rory and I want to see a play on Broadway."

"Yes, yes, yes," muttered the Doctor, giving his proof another look. "Off to Broadway for a bit, then right back to planning. I really can't let this time stream stay the way it is. It could destroy one twelfth of the universe if things get out of hand."

Amy swung around the door. "If you let me and Rory sneak into their house we can tell you how crazy things are, how mad Jonathan is…"

"Nonsense," The Doctor said, waving his hand at her. "Besides, I gave Clary my number. She'll call me if something horrible happens."

* * *

Clary clung to the scrap of paper in her hand desperately as her father approached her and Jace. It seemed silly, to cling to something so insubstantial and meaningless, since Mr. Smith was in no way capable of protecting her from her father, but it was something. It was a testament to the fact that _someone _cared about her, _someone _was thinking of her wellbeing, that somewhere, there was an adult who would listen.

_Listen to what? _that mean voice in her had asked. _No one will ever believe you if you told them the truth. That you're not really human? That your father, who happens to be the supreme ruler of a race of superhumans is abusing you and no one cares? No, little girl, you're on your own. _Clary's eyes moved inexorably to Jace whose shoulder was brushing up against hers. _Well, not entirely on your own. _

"Jonathan tells me you were speaking to someone after school?" Valentine asked, his eyes dark. "He says you were speaking to a woman, and that she seemed very friendly with you two. Making friends, are we?"

"No," Jace said at once. "We have friends already."

"You think so?" mused Valentine, smiling condescendingly at Jace. "Whatever friends you had belong to me now. Everything you had belongs to me now, though sometimes it seems you forget that."

"She was just a nice woman waiting around for her friend," Clary said defensively. "We didn't tell her anything about…_us_."

"She wouldn't believe you anyway," sneered Valentine. "But that isn't what concerns me, children. You see, if you were talking to her, who else have you been gossiping with?"

"No one," Clary said quickly, shaking her head and backing up a bit more. She felt her back brush the wall of the dining room and knew they were in trouble. "We don't talk to anyone."

"I find that hard to believe," Valentine said, glancing over at Jace. "Jonathan also tells me you were talking to this Mr. Smith again."

"_He _ran into _us,_" Jace said, exasperated. He hated when Valentine did this, drew out the punishment, putting them both on edge. "We didn't talk to him, just asked him to look over our homework for some help with the problems-" Jace clamped his mouth shut when he realized what he'd said, but he knew there was no way to take it back.

"You still can't do your math homework?" Valentine shook his head. "I'll deal with that later, but still, I must impress upon both of you my concern that you're telling lies. If you're talking to this random woman, if you're talking to this teacher, what are you telling them?"

"We're not telling anyone anything!" Clary squeezed the paper in her pocket tighter.

"Liar!" snarled Valentine and then grabbed Jace's shirt. Jace struggled a bit, but not enough to have Valentine go after Clary; Valentine jerked Jace's shirt up, revealing the ugly whip lashes. "Telling people about these, are we? Letting those Mundane teachers know all about our family secrets?"

"No!" Clary cried desperately. "We haven't told anyone, I swear! I'll swear it on the Angel if that's what you want. No one knows."

"I don't believe you, Clarissa." He tossed Jace back against the wall. "Perhaps I've been going about your punishments wrong, perhaps leaving marks is asking for trouble. Shall we try something new?"

"Why?" Jace demanded rashly. "What have we done wrong?"

"You spoke when I didn't tell you to," he answered simply. "And, as you've already admitted, you couldn't handle your math homework again. I'm really growing tired of having your miserable failure thrown in my face. What must those teachers think of you, of our family?"

"But we got full credit!" Clary snapped. "Mr. Smith didn't take points away for asking."

"You shouldn't have had to ask in the first place. Now, I'd like both of you to sit on the couch with your shoes and socks off." Valentine shrugged off his coat, and when he saw them standing before him, he pointed. "Go."

As they went, Clary's fingers rubbed the paper. _Think of something nice, think of something pleasant and fun. _She thought of the nights she'd had with Jace, curled up beside him, listening to the steady beat of his heart. That was nice. _Think of Jace. _

Beside her, sitting on the couch, Jace looked nervous. He was running through his head everything Valentine had said and their current position. No shoes and socks was an odd request, though not completely unwarranted. It worried him a little though, since so many nerve endings were in the feet; it was a delicate place and if Valentine chose to attack there it would be painful. He looked over to Clary, fiddling with something in her pocket, and he felt the wave of protectiveness he always felt when he saw her. Not something overpowering and possessive, but just that reminder in the back of his mind that Clary wasn't used to pain like he was, and, though he certainly couldn't protect her from it all, he would try to protect her from the worst.

Valentine joined them, a knife from the kitchen in hand and a bottle of rubbing alcohol. Jace swallowed. _This isn't going to be clean, _he thought, wishing suddenly Valentine had a stele in his hand. At least those blades burned the skin back together.

"So, who would like to go first? Wait, let me guess…Jace, I'm sure you're willing to go before your little lady?" Jace nodded mutely, staring down the blade. "Give me your foot then." Jace lifted his left foot and carefully placed it before Valentine, who gripped it around the ankle like an iron manacle. With the other hand he dipped the knife in alcohol and ran it through an open flame. Jace jumped when one of his fingers separated his biggest toe from the one next to it.

_Definitely going to be messy, _was Jace's last thought before Valentine sliced into the delicate skin between his toes with the knife. It was more pain than Jace had expected, and he let a shuddering gasp escape him, but it didn't seem to reach Valentine who continued on to the next gap, and the one after. It was the serrated edge that really did the work, and Jace squirmed against his will every time Valentine cut his skin. When he finished one foot, he began the other, making sure Clary saw.

When he finished, he surveyed the work before him with a frown. "Don't bleed on my carpets," he said, and then turned to face Clary. "You next, my dear."

Terror choked up Clary's throat. "Please, Father, why won't you listen…"

"Give me your foot, or I'll do Jace again, and next time, I'll slice the muscle." He watched Clary's face resign and knew that he'd won; she placed her foot gently in his lap and looked at him with round, green eyes. Valentine saw a bit of Jocelyn there, and he was grateful for it. His anger at his wife had been building over the years, and now, he had a perfect replacement to take it out on. "Don't scream, Clarissa; I don't want the neighbors asking who makes all those noises."

Clary fought every urge she could to scream, and even then, small sounds kept escaping her mouth, earning her disapproving looks from her father. She could feel the tissue and muscle being torn as he went, she could see little drops of blood dribble onto the floor, and she could hear her own raw moans. Beside her, Jace was looking furious, like he wanted to lunge across at Valentine, but she knew he wouldn't; it wouldn't get them very far if he did.

"This seems all in order," said Valentine as he finished the final cut between Clary's small toes. She snatched her foot back and squeezed the toes together in a vain attempt to staunch the pain. "Oh, don't, Clarissa, you look like a child when you do that."

"It hurts," was all she said, and very carefully, put her feet down. Clary made to stand, but her feet gave out beneath her and she toppled forward into his father. Valentine snarled in disgust as he caught her and then tossed her back on the couch.

"Can you not even stand, Clarissa? Are you so helpless?" he demanded, rising up before her and casting a threatening shadow over her crumpled figure. "Again and again, you remind me why I don't want to claim you as my daughter. Jace, get her away from me."

Jace rose unsteadily to his feet and levered Clary up. She had to lean against him dangerously, almost toppling him sideways. Under Valentine's eye, the two hobbled from the room and into their bedroom. Jace set Clary down on the bed and then collapsed beside her, staring at his mangled feet. Clary stared down at the floor, her lips trembling as she held back her cries of pain.

"You should elevate your feet," Jace suggested. "Stop the blood from gathering in your toes and leaking out if you can." Jace patted the bed beside Clary and she leaned back. "You did very good, Clary. You didn't scream, you didn't make him angry."

"I guess that's something to be happy about," muttered Clary. Her hand strayed to the paper in her pocket and she removed the phone number Mr. Smith had given her. "Do you think I should mention the tutoring to Valentine?"

Jace chuckled darkly. "Yes, now seems to be the opportune moment to mention getting math help. While we're at it, I'm going to ask for a car, a passport, and…hell, why not some condoms to top the night off?"

"Jace!" Clary cried, punching his side, but relaxing at the thought. "I don't know why I kept this, really. It's not like we can get the tutoring we need anyway. Valentine thinks we're gossiping with Mr. Smith, he'll never let us be alone with him." But Clary couldn't let the paper go.

_You're just clinging to desperate hopes and dreams. He's a math teacher who wears a bowtie and keeps a box of cookies in his desk. You're a girl whose father is teaching her how to kill by beating her. Those two worlds don't clash. _

Later that evening, Valentine returned, this time, carrying a stele, a pen, and a piece of paper. Clary and Jace had lurched up, watching him warily. Valentine eyed them both dispassionately, but pulled a chair up to sit before them. "Clarissa, it's time for you to serve my wishes, and, in so doing, perhaps earn Jace a little reprieve from his starvation."

Clary leaned forward thoughtlessly; it was her fault he was starving in the first place. "What do you want?"

"I've decided the best way to keep you two quiet is a rune rather than a beating. You're going to draw me a new rune, not a normal Silenceing rune, something a little more exacting. I want to limit how much you two can speak a day." Valentine smiled at Jace's indignation. "I think it might even teach you to appreciate that you can speak at all. So, Clarissa, make me the rune, and I'll let Jace eat again."

Clary didn't have to think about it; she snatched the pen from Valentine even though Jace made a small protesting noise. It was much harder to create runes under her father's cold eyes, and she'd only done it once before. He was a leech for any dreams and hopes she had, he drained the creativity out of her, and it left her empty and unable to create. It was now only fear of repercussions that drove her onward.

"I'm not going to wait all day, Clarissa," warned Valentine as her hands trembled over the paper. "I knew your Mundane studies were abysmal, but if you can't even make a rune, I may have to reevaluate _my _teaching techniques, and you don't want that."

Clary's hand moved aimlessly at first, tracing lines here and there, not really sure she had an idea in mind. She thought of all the things she'd like to say, and all the people she'd like to say them to. She thought of Valentine, and how much she wanted to speak her mind; of her mother and how she wanted to scream and shake her until she finally understood. She thought of Simon, and Luke and Magnus, and she didn't even know if they were alive, but she wanted them to be, just so she could talk to them. She thought of Isabelle and Alec and Max, and how she wished one day her father would let her seem them again, just so she could tell them how much she loved them. She thought of Jace too, and how there never seemed just the right word to tell him how grateful, how honored, how blessed she felt to have him. And, oddly enough, she thought of Mr. Smith and his friend, Amy. She didn't know why Mr. Smith came to mind, only that she got the oddest feeling when she was around him, that he knew more than he was saying.

Clary thought of all these things, and then thought what it meant to lose them. How, since her father's victory on Idris, her voice had withered and died. No one listened to her anymore, no one cared what she had to say. She was all but mute now, all but for Jace, and that was how it was going to be from now on. She would silence herself to the world, she would have only enough words for Jace and he for her.

Her hand was moving across the paper now, and when she looked down at the rune before her, she beheld a mess of circles. A large circle with many smaller circles within it, two lines crossing each other like a distorted X. The rune didn't really look like anything she had ever seen, it didn't even look like the language of the Angel. Clary stared at it in utter shock, confused at what she had drawn.

"What is that?" Valentine demanded, snatching the paper back from Clary and staring at the circles. "This is _not _the language of the Angel; this looks like _warlock _rubbish."

"It-it's a rune," Clary stuttered. "I sweat, it's a rune!"

Valentine grabbed the back of Clary's head by her hair and pulled her forward. "You had better hope it is, Clarissa, or I'll try _my _best to make the rune, and I'll practice drawing it on you with my stele."

"Please," Clary croaked, feeling her father's fingers twisting her hair in a merciless grasp. "It's the rune you asked for, just-just draw it on me."

Jace had moved forward and had reached forward to stay Valentine's hand. "Try it on me first, Valentine, if it doesn't work we'll know."

"Jace, don't-" Clary pleaded. She had discovered the hard way what had happened to people when her runes failed. Valentine had once ordered her to make an Immobilizing rune, and her first attempt had failed. When applied, the rune had turned her skin to fire and a fever burned through her body. She had made so much noise, screaming, tossing and turning as the fire burned through her, that Valentine had had to tie her to the bed and mark her with a Silencing rune. She couldn't risk the rune being a failure.

"Me first," Jace said louder still, and then offered his arm.

Valentine offered Clary a sad smile and then jerked Jace off the bed. Jace couldn't support his own weight and tumbled unceremoniously to the floor. Valentine lifted Jace shirt up just enough to see the patch of golden skin that was the small of his back. Jace struggled just a little, but knew that Valentine could easily mark Clary instead, and she'd already been through it once. Valentine murmured some words, and Jace felt the familiar burn of the stele, though it felt more binding, even though it had been months since he'd been marked, and waited tensely for the fire that would surge through him if Clary had failed.

Both Valentine and Jace waited, but as the minutes ticked by and nothing happened, they both assumed the rune had worked. Valentine traced the strange circular rune, confused by it. Normally a rune, even if once created by Clary, could be read by a shadowhunter; this rune didn't translate to Valentine. It was just circles in circles in circles. However, when Jace knew that he wasn't about to convulse into withering pain, he rolled away from Valentine, looking like a cornered animal.

"My, my, my," Valentine said, looking slightly impressed. "Clarissa, it seems you can still surprise me. I'm not utterly ashamed of you." This seemed to be rather amusing to him because he spun the stele around and gestured for Clary to show him her back. Clary didn't bother being humiliated or outraged at his comment, just offered him her back and waited for the sting of the stele. As he applied the rune, Clary felt a spark where the knife touched her and then heat race from her back up and down her body. She curled forward and whined just a little.

"I'm rather pleased by all this," Valentine decided, standing up and surveying the children. "Perhaps I might not have to punish you two for the math failure after all. Keep yourself quiet and occupied for the rest of the evening and I might feed you a hot meal."

The new rune Clary and Jace now bore had taken what little freedom they had and quashed it, successfully suffocating them. They had enough words to share between each other at night, a few moments to whisper hopes or dreams, and enough to appease Valentine's demands of them. The silence, though, had left Jace and Clary with little other to do than curl up beside each other and study or read.

At school, they barely spoke, they couldn't afford to. At first, the teachers had liked it, and had thought the children were just being studious, however, it became offensive. Teachers would ask them to answer questions, and they would shrug or look away or shake their heads. When the teachers demanded answers they would give blank looks or one word answers. Within the week, Clary and Jace had both been sent to the principal's office for insubordination.

When Valentine received the call home on Friday that they were being rude and disobeying their teachers, he was quick to take action. Though they pleaded that it wasn't their fault, that it was the runes that had kept them silent, Valentine had blamed them, saying that they should have answered their teachers and shut up with each other. When he beat them, they couldn't plead with him to stop, they could only moan and grunt with each blow.

* * *

"Look at this!" the Doctor exclaimed, staring at a screen on the main control. "_Look at this_! This is _impossible_! This is _unheard _of! This is-" the Doctor spun around, expecting to see Amy and Rory waiting for him to explain, but was instead met with the empty room of the Tardis. He glanced around, checking the corners, the staircase, even the area beneath the main floor, but there was no one. "What do I keep those Ponds around for anyway if they're not even going to be here when I'm making my deductions?" As in response, the Tardis groaned and the counsel flashed in green. "Exactly!" the Doctor agreed. "That's exactly what I'm saying."

The Doctor glanced at the clock imbedded in the counsel and saw it was five in the morning. _Well, we are up rather late, _the Doctor thought, and then turned back to the screen.

What had so shocked him in the first place was the spike in radiation that had woken the Tardis. He had been taking scans of most of New York since their arrival, and had already picked up the rather massive spike that must have been Valentine's portal to Idris. It had told him both where Jace and Clary were, as well as allowed him to monitor when people traveled through the dimensions. He had been trying to coax the Tardis into tracking the signal and then heading off for Idris himself, but she had been touchy as usual and refused to follow it. He supposed she wanted him to stay in New York longer.

However, this radiation aside, the Tardis had recently registered another, very unique type of signal. It had been so shocking to the Doctor in the first place because when the Tardis received it and, after a few days, transposed it on the screen, it was Gallifreyan. The Doctor stared a long time at the image before him, mostly because it had been well over a hundred years since he'd received a message in Gallifreyan, aside from the note River had carved into the mountain, and his mind, for all its speed, couldn't quite process the meaning.

_There can't be another Timelord,_ he reasoned at once. _I'd know it if there were, I'd be able to feel it. I'm the last…_

The Doctor gave himself a good shake to push the memories away and returned focus to the screen. "But no one alive can read or write Gallifreyan, so, who's sending me messages? Where is the signal coming from?" The scream flickering and presented a map of the region, locking in on none other than the pent house where Valentine Morgenstern made his home. "I should have figured this would be coming for you, Valentine. Where did you get my language from?"

However, the screen couldn't tell him that, and he gave a frustrated groan. It was no coincidence that this was cropping up around the shadowhunters, at least no coincidence that he was there to see it cropping up. Still, it didn't make any sense; no matter how advanced the shadowhunter culture was, it would take a super genius, at least ten times smarter than the average human, to begin to understand Gallifreyan.

"Well, what are you trying to tell me, anyway?" asked the Doctor and drew the image of the words back up. He frowned at it, feeling a rather uncomfortable feeling in stomach. "_Speak_," he read aloud.

For an hour, the Doctor sat before the screen, staring at the word and frowning. None of it was adding up no matter how he drew the conclusions together. Unless a shadowhunter just stumbled over the word completely by accident, something was causing the presence of this word. He ran his fingers through his hair.

"The only thing that could cause a rift like this is me, so brilliant for me, I guess," the Doctor snapped, leaning back and staring at the word. "Speak, eh? Speak to who? Speak about what?" the Doctor jumped up and looked again at the clock. It was Monday, he had to be at school that day; he'd see Jace and Clary. "Speak to them?" The Doctor stared a moment longer at the screen. "Parent Teacher Conference Day…Speak to Valentine?"

The Doctor jumped up, clapping his hands together ecstatically. "Speak to Valentine, give him a start, that's what I'll do!"

With another rather mad laugh, the Doctor grabbed his coat, and decided on a top hat, since the weather seemed foul, and raced out the door. He'd left Amy and Rory instructions to go out and have some fun around New York, and that he'd be late coming home. As he headed for the school and Jace and Clary and , later, Valentine, his mind was bursting with a plan.

_I've got a plan! _the Doctor thought to himself. _I've never had a plan before; god forbid Valentine Morgenstern try and best me when, for once in a thousand years, _I've_ got a plan._


	5. Parent Teacher Conference

**Hey everyone, sorry I'm posting one these notes so late in the week, but I don't think I'll be able to post the next chapter for this on Wednesday like I usually do. I'm smack in the middle of finals and I've been buried in chem and physics for most of the week. I'll do my best to get the next chapter up sometime later, hopefully by Friday.**

Parent Teacher Conference

_Oh, now what's this then? I love this. A big, flashy-lighty thing. That's what brought me here. Big flashy-lighty things have got me written all over them. Not actually, but give me time…and a crayon_

_-The Doctor _

"I hope to see your parents tonight, children!" the Doctor called over the ringing bell, and then added rather proudly, "I'll give you five extra credit points if they come, you know, and besides, I've got jammy dodgers."

A few of the children rolled their eyes; they had since accepted how odd Mr. Smith was and had simply learned to get on with his outrageous outbursts. Clary gathered her things rather slowly, hoping to catch Mr. Smith and ask him, plead with him, not to mention tutoring to her father. She knew if Valentine got wind of the tutoring he'd blame them, and she and Jace couldn't afford any more. Jace hung back as well, figuring that Clary shouldn't waste too many of her words, so he could speak as well. Once everyone else had left, Clary and Jace approached Mr. Smith; they waited silently for him to notice them.

The Doctor jumped when he saw them, his eyes glowing. "Clary, Jace, what can I help you with? Have you spoken to your father?"

Clary felt her throat constrict. "Well-well yes, I have, and he's really not sure we have the time." Even to Clary, the words sounded weak, clearly a lie. "He's not interested."

"Are you so sure?" the Doctor might have been a fool when it came to humans, but he recognized fear when he saw it. He had the urge to reach out and touch her thoughts, just to see what she was holding back, but he withheld himself. It was rude to intrude on peoples thoughts. So, instead, he reached out, taking in her emotional climate. He was concerned when, from both Jace and Clary, he felt only raw terror beneath shaking nervousness. "You know, there's nothing to be worried about; getting help for math is normal. I can speak to your father."

"You don't have to," Jace said quickly. "He just doesn't have the time for us to be picked up late. If there were any other way, but we just can't."

Again, the Doctor sensed Jace's fear, and it sent a spike of outrage through him. The Doctor didn't turn away terrified children. "Is there something else you'd like to tell me? You two have been awfully quiet this last week."

_Oh, no, no, no, no, _Clary thought, terror griping her. _He knows, and if he knows, the other teachers will know. They'll tell father we're acting odd and he'll think we've told. _"My mother's gone away on business, and it's just been odd in our house," she said quickly and Jace nodded in agreement.

The Doctor knew Clary was lying as soon as she'd opened her mouth. "It's just that usually you're here during lunch for help, and I haven't seen you in days, and I notice you're hand isn't healing up right."

"It's fine!" Clary said sharply, and she felt Jace's incredulous eyes on her. She continued much calmer "My father took me to the doctor and said the bones needed to set, were all. It's fine."

"Broken fingers?" the Doctor asked, eye brow raised. _Had Jonathan grabbed her hard enough to break the bones? _"Pity that, must make it hard to write. Which reminds me, your homework was a little sloppy yesterday, I take it the fingers are the cause of that?"

Clary knew the reason her homework was a mess was because the day before, Valentine had grown furious at her for drawing a rune wrong during practice and had made her repeat the same rune again and again for three hours. Her wrists were cramped by the time she'd started calculus. "Yes, I'm really sorry about that."

"Nothing to be sorry about, don't panic about it." said the Doctor, catching the note of distress in her voice. "Really, you two look a little ill to be honest. Perhaps you shouldn't come to school tomorrow. You're awfully pale."

"We're not sick; we like school." It was true, since school was now the only place they were free of Valentine. "Just a little nervous about conferences is all."

Carefully, gently, the Doctor reached out and took Clary and Jace's wrists. "You've got nothing to be nervous about; you two have been doing excellent in my class. What would you have to worry about?"

The answer on tip of both their tongues was Valentine's wrath if they were performing below his standards. However, they couldn't say that. Jace struggled to find words, but he didn't know enough about Mundane life to formulate an excuse. Clary, though, snapped to attention. "College. We're both trying to get into a good college, and an ivy league university will expect all A's."

"Understandable," shrugged the Doctor, not thinking much of the excuse. "But nothing to be worried about. And, if you're so concerned about your grades, there's always help you can get. My door is always open."

For a moment, Clary thought there was a double meaning to Mr. Smith's words, but shook it off. As far as he knew, she and Jace came from an affluent family, with a loving mother and father and brother. Clearly, they didn't need an open door. "Grades are just important in my house."

"As they should be," agreed the Doctor. "Oh, well, I won't keep you, off you go. I'll see your father tonight, then."

Once Jace and Clary had left the Doctor sat down, his face serious. He had never been great at reading humans, since they seemed to him, so fleeting, and anything they felt was but a second in his life. However, Jace and Clary were different; they seemed oddly quiet, and the silence spoke volumes. He couldn't say what was wrong, but knew only that the sooner he worked out Valentine's existence, and, more importantly, the sooner he got the two children away from him, the better. Something about the fear in Clary's eyes and the helplessness in Jace's had set him on edge.

The Doctor ran a hand through his hair, fussed with his bowtie, then turned to face the board and began work on his own rune.

* * *

Amy and Rory, after finding the Doctor's note, for some reason, taped to the coat hanger by the door, had decided a walk through New York was in order. Amy thought it might be an excellent addition to her article and besides, she and Rory couldn't stay locked up in the Tardis all day while the Doctor got to have his fun, pretending to be a teacher. Outside, the sun had decided to show its face and a fair breeze was keeping the heat at bay.

"You know, if we ever had to leave home, I'd like New York," Amy mused. "There's something so exciting about it, you know?"

"You've seen the whole of time and space collapse around you, and you think New York is interesting?" Rory raised an eyebrow skeptically. "You think it might be a little boring after that."

"You know what I mean, Rory," Amy sighed, giving him a playful shove. "It's exciting in a _normal_ way. There's so much life compared to back home, so much to do and see."

Rory gave the New York street a glance, but he didn't seen anything that really impressed him. He figured that after you traveled with the Doctor for so long, nothing was that surprising anymore. "More life, maybe, not more exciting."

Again, Amy shot him a look. "One day, Rory, you and me are gonna have to stop running around with him. One day, we'll have to settle down and start a real life, not Doctor Life, but a real…_life._"

Rory was about to tell Amy he'd start that life whenever she was ready, but his voice died in his throat when he spotted something slightly peculiar, even by Doctor standards. Amy followed his line of vision to a huge cathedral, with what appeared to be odd Latin writing over its gates. However, as she focused on it, the Tardis translated and she read The Institute in thin lettering over the gates. It wasn't the writing, though, or even the fact that the cathedral was clearly not what it seemed that drew her attention. It was the three children outside the building, the three children dressed in worn black clothing, sparring with each other, with very sharp weapons.

Rory gave Amy a sidelong look. "I know we have to get a real life eventually, but we're not talking about right now, right?"

Amy shook her head. "Nah, real life can wait," she said, and ran to the gates. They skidded to a halt just in time to catch the older boy speaking.

"Max, you need to keep your feet apart, but don't shift your weight onto your heels. You won't be able to move!"

"Alec," the girl said, who was seated on a bench, shoulders slumped sadly. In her hand was a whip and it curled about her wrist like a snake. "Give him a break, he's tired."

"Tired or not," the boy Alec said, "doesn't make a difference. If Valentine comes back and finds that Max hasn't improved he'll punish him. How will you feel then?"

"I'm not saying we let him quit, I'm just saying let him take a break and _explain_ yourself, not just scream at him." The girl stood up, and Amy, thought she was very intimidating, but seemed very tired and her shoulders slumped still. "Max, come here and I'll show you how to balance your weight all on your toes."

The little boy, who Amy was eyeing like a hungry mother, gave a frustrated sigh. "I don't want to do it anymore! I don't want to keep fighting, I'm tired! I want Hodge to teach me! I want Mom and Dad to teach me!" The boy drew a shuddering breath. "I want _Jace _to teach me!"

"Jace?" Amy and Rory said at once and exchanged confused looks.

"Well, it could be any Jace," Rory said, but even he doubted his words; something about the children training with weapons, hidden behind a strange language, made them both think that they could only be referring to one Jace.

"I'm sorry, Max," the girl said, turning his face up to hers. "But you know Hodge, Mom, and Dad aren't here. Hodge is dead and Mom and Dad are-"

"Izzy!" Alec warned.

"They're in Idris somewhere," Isabelle said firmly. "Valentine is keeping them hostage until they drink from the Cup. As for Jace, Max, he could be anywhere…"

Isabelle turned away from Max's large, round eyes, unable to face the accusation that lingered. She hadn't forgiven herself for letting Valentine take Jace and Clary away in the aftermath of the war. It had been haunting her for months now, in both her dreams and her waking hours, and she felt oddly responsible, especially for Jace, since he was her brother. Her last image of him had been most disturbing and always swam up before her eyes whenever she relaxed for even a moment.

The shadowhunters left fighting were struggling with the press of the demons, and Isabelle hadn't cared anymore that she was too young to fight. She locked Max in her room and picked up her whip and gone to join the fray. All about her she saw enemies and allies falling, proud soldiers torn to bits, screams filling the night air, blood running in rivulets about her feet. She spotted Alec in the disarray and rushed to his and Magnus's aid, only to have the demons fall back suddenly.

There were moments of confusion when it seemed like nothing made any sense. Hopefully, Isabelle thought that maybe Clary and Jace had stopped Valentine and Jonathan, maybe this nightmare was over. She turned to face her brother, ready to ask if they should go find Clary and Jace when a voice, magnified five times over, rent the air.

It was Valentine, and he was riding down to meet them on a horse. Isabelle screamed in terror when she saw the unmistakable red head of Clary seated before her father. From what she saw, Clary was bound and gagged, her head bobbing listlessly against her father's chest, and she seemed oddly bemused by the scene before her, as if she didn't understand what had happened. From behind Valentine emerged Jonathan, and seated before Jonathan, was Jace.

These were the last moments Isabelle had gotten of her bother. Jace was more aware than Clary, but he was bound with runes, not rope, and he couldn't maneuver out of Jonathan's grip. She'd watched Jace twist away from the other boy, only to be struck sharply across the face. When he turned a glare at Jonathan, the demon boy pulled out a small knife, and playfully traced a line down Jace's cheek, over his throat, to his frantically rising chest. For a moment, Isabelle thought Jonathan was going to kill him, that he was going to flick that knife around like she had seen him do before and drive it into Jace. Whether that thought was running through Jace's mind or not, Isabelle would never know, because at that time Valentine turned to Jonathan, beckoned him forward and placed Clary's limp body behind him.

Isabelle didn't miss how Jace's eyes traced Clary's path only to return to Valentine, who smirked at him. Jonathan and Valentine exchanged words, and Jonathan turned his horse about and he, Clary, and Jace set off at a brisk gallop for the city. Isabelle had followed the sight of Jace's golden hair into the distance, and her heart at gone with him. Wherever Valentine had sent Jace and Clary was far worse than where she was.

Now, Isabelle stood before her little brother, who had worshipped Jace for as long as he'd known him, and she could say nothing to comfort him. She shrugged hopelessly. "Where Jace is, Max, he'll be with Clary, and those two will take care of each other. They love each other."

"But what about what Jonathan said-?" Max began, but Alec shushed him.

"Don't listen to Jonathan, he's just trying to scare us," said Alec firmly. "If he really does know where Jace and Clary are, he's not going to tell us."

"You don't think they're in Idris?" Max asked. "You don't think they're with our parents?"

"No," Alec said and knelt down before Max to hold his eye. "I think Valentine tucked Jace and Clary away somewhere, and I just don't know where. But, I'll tell you something, Max, I think we could find them if we tried. I think that the three of us have it in us to go find Jace and Clary."

Max's chest swelled with pride. "I'll practice more, Alec, that way, when we try to find them, we can fight Jonathan."

Alec nodded proudly. "Alright, Isabelle, you want to show him?"

Isabelle smiled warmly at her brother and was about to show Max how to balance his weight when she saw a head full of bright red hair. Her heart stopped a moment, and wildly, she thought, _Clary?_ Wordlessly, she pointed and then took off, jumping the bushes that were obscuring her view, Alec and Max right behind her. However, the burst of frantic energy was cut short as Isabelle scrambled up to the gate, her brother on her heels.

_No, _Isabelle thought, her heart breaking, but then she drew a shuddering breath, realizing the woman was smiling at her. _They can see me? _She felt Alec and Max draw up to her, silent as ghosts, thinking the woman and man on the other side of the gate were blind to them, but Isabelle shook her head mutely, and the woman winked at Max.

"You're not Clary," Isabelle said blankly, taking in the sight of the woman and the man beside her.

"Well, no," the woman agreed, rolling her eyes playfully. "But, I might know where to find her."

* * *

The Doctor smiled at his handy work on the white board and returned to his desk, to fiddle with the small piece of technology in his lap. He shook it, listening for loose pieces, tweaked the sensors, and finally, frustrated, removed his sonic screwdriver from his coat pocket and adjusted the settings with that.

"Look at you, you beauty," the Doctor said, eyeing the tracking device. "You're going to do great things you know. You're going to be brilliant."

"Who's brilliant?" asked a voice from the door.

The Doctor jumped, his hand closing over the tracking device, and he leapt to his feet, adjusting his bow tie. He was faced with a very large man, both tall and wide shouldered, with a pair of very cold eyes. The Doctor's eyes took in every inch of the man in less than a second; the straight, white blond hair, the sharp angles of the face, the dark eyes, but it was more than that. There was an unmistakable air of power about the man, and his every action was that of a hunter, a soldier. The Doctor could feel his skin tingle as he sensed something not human. This was Valentine Morgenstern, the man that should be dead.

"Me!" the Doctor said, acting surprised that Valentine didn't realize he'd be referring to himself. He rushed up and kissed the air on either side of Valentine's face. Valentine stared at him like he were a madman, but the Doctor didn't notice. "Of course I'm taking about me, I'm brilliant. No one ever tells me that, so I figure I might as well tell myself. Just to keep up morale, you know."

Valentine, though a shadowhunter and trained in surveillance, was no nearly as fast as the Doctor, and he took a moment to consider his counterpart. The man, Mr. Smith, was young, much younger than Valentine had been preparing for, and he seemed to wear a perpetual smile. Valentine didn't necessarily like the smile, since he thought it belied something else, but he couldn't tell what. Aside from his smiling, empty face, Valentine noticed the man wore an odd arrangement of clothing, not really suited to teaching; it was something about the coat that was a century late or so late. However, Valentine, for all his senses and training and years hunting things down, didn't think for even a moment he was in the presence of a fellow soldier. All he saw when he looked on Mr. Smith was an odd, young man who smiled too much.

_This idiot, _Valentine thought smugly. _This is the man who outsmarts my children and thinks himself brilliant. He doesn't know a thing of life, of danger, of the real world. He thinks his books and his calculation will save him. A Mundane if I ever saw one._

"Some might call into question your ego," Valentine pointed out, joining the Doctor at the desk.

"I can't imagine why if it's earned," said the Doctor and then touched his bowtie. "I'm Mr. Smith, the calculus teacher here, and you are…?"

"Valentine Morgenstern, Clarissa's father and Jace Lightwood is my ward," he said calmly, giving Mr. Smith's bowtie a disdainful look. He prided himself on his clean, neat appearance, and a bowtie wasn't anything he would ever have considered wearing. "A bowtie is little 90's, don't you think?" he asked amicably all the same.

"Bowties are cool," Mr. Smith said promptly. "Einstein wore a bowtie, and he was cool."

Valentine raised an eyebrow in response, since he didn't actually know what Einstein was famous for. "A differing of opinion is all. So, I understand my daughter is having some trouble with your class."

The Doctor laughed. "I wouldn't say _that_. Clary is doing quite well, and she's clearly dedicated to the course; she and Jace are in here every lunch period with questions. Her test scores are consistently some of the highest in the class, and her homework is exceptional."

"She tells me her grades are B's," drawled Valentine; clearly he didn't approve of such grades.

"Yes," agreed the Doctor, pulling out a stack of exams from the previous week. He removed hers and flicked through it. "She has expressed some concern with that, and I've offered her and Jace some tutoring if they're interested."

"Did you?" asked Valentine, surprised, and he wondered what else they had been hiding from him. "I was unaware."

"Oh," said the Doctor, and he knew then that Jace and Clary had lied earlier, though he didn't know why. "They said they were too busy to stay after school, and they hadn't asked you yet if there was time for me to meet them outside school."

"We keep a busy schedule," agreed Valentine. "I was unaware that my children were in such need of tutoring in the first place. Perhaps, you should contact me directly, Mr. Smith, when you wish to discuss educational matters."

"I'm sure the children forgot," the Doctor waved it off. "You know how kids are, with their texting and their vampires and their…_jammy dodgers_. Would you like a jammy dodger? I keep them in my desk in case I get a bit hungry. Teaching, it drains you." The Doctor retrieved the tin, and slipped the small tracking device into the jam between the cookies. He offered it to Valentine, taking a large bite of his own. "They're fantastic."

"That's a British sweet, is it not?" asked Valentine, taking the cookie and withholding his mild disgust.

"Oh, well, yes, I suppose it is, not that I'd notice," shrugged the Doctor, polishing it off. "I find they're the most useful type of sweet you could possibly eat, regardless of where they're from." Valentine noticed the Doctor smiling, and for a moment, something distant passed through his eyes, some memory of some other place. "They're filling, tasty, probably have other endearing qualities that are worth mentioning." _Like a fake explosive detonator? _he asked himself.

"I notice only because you have an accent, Mr. Smith, northern, if I'm not mistaken," Valentine said, wondering what the man was going on about. He eyed the cookie, and, after seeing the beaming look from the Doctor, took a bite. "I have traveled through much of Europe, where are you from?"

"Lot's of places have a north," said the Doctor mildly, thinking fast. "London."

"London?" Valentine finished the cookie. "You've certainly come a long way."

"Not really," laughed the Doctor for some reason. "It's still 2007 as far as I know."

"If you're going to measure by time, I suppose not," Valentine returned, keeping his face blankly polite to hide his inner dialogue. "Well, back to my children. I've seen Jace's test scores, and he seems to be doing well, though that last exam was rather disappointing. Have you had any trouble with him?"

"Trouble is strange word, isn't it?" asked the Doctor curiously, giving Valentine a sudden hard look. "Jace and Clary seem to be performing well in my class, yet I see you will not be dissuaded. I have not had any _trouble _from either of your children."

_And who do you think you are to have an opinion of my children, Mr. Smith? You're nothing but a pathetic, mindless human. _"It is surprising to many teachers here that before Jace and Clarissa were enrolled here, they were rather…insubordinate. Skipping lessons, poor manners, foul behavior; it had driven my wife almost to the brink just to deal with them. I find I must keep a _very _close eye on them or else they may turn back to bad habits."

Again, the Doctor had a hard look. He knew Valentine was lying. "Perhaps you ought to trust them a bit more?"

"Trusting them thus far has only gotten me lies," said Valentine sharply.

The Doctor grinned. "If they were going to tell you the truth all the time, they wouldn't need you to trust them."

"I have given it thought," Valentine finally admitted, after having worked out what Mr. Smith said. "However, I find it is still wise to pay particular attention to their school work. How about I give you my phone number, and you can contact me once a week, to let me know how Clarissa and Jace are doing?"

The Doctor got the feeling that any call he'd make regarding Clary and Jace wasn't going to be met well on the other end of the line. "If you'd like, but if you're that interested in their education, I'm more than happy to keep them after school once a week, just to review major concepts."

Valentine frowned. "Let me know how their next quiz goes, and I'll let you know then."

The Doctor clapped his hands together. "Excellent, excellent; well, this has been a rather enlightening talk, hasn't it? Very nice. If you'll excuse me, Mr. Morgenstern, I've got to go back to my work. Laziness doesn't breed brilliance." He winked and jumped up to the board, pausing, waiting, waiting for Valentine to see the mark he'd drawn on the board, waiting for that moment when he knew he'd be right again.

Valentine had followed Mr. Smith with sharp, calculating eyes, and he was about to leave when he saw the image on the board. For all of ten seconds, he stared in shock, his mind blank as he tried to process what he was seeing, and why it was there. When he blinked, his mind jumped into action. "What is that? It doesn't seem like any math symbol I've ever seen."

The Doctor grinned to himself. "What, this?" he asked, and pointed to the drawing on the board. It was the Gallifreyan symbol for _speak_, the very same symbol that he had seen on the Tardis screen that morning. "Why do you ask?"

Valentine considered his words carefully. "I've seen it before. Ancient culture studies." _If Clarissa drew there that I'll wring her throat twice over. _"Biblical, isn't it?"

"This?" Mr. Smith laughed. "No, no, no. This is mathematical, scientific even. Archeologists found it painted on cave walls in the earliest civilizations. They think it has to do with space, or planetary movement. That's what all the circles are for, all the lines too. Tracking the stars…"

"And you study this?" Valentine pressed. _I'm going to wring her throat anyway; lying little brat. This is no rune._

Mr. Smith smiled, and for the first time, Valentine felt that he was in the presence of something not human. It was like the man's smile held a world of knowledge, secrets, and truths, and none of it belonged in this world. "Oh, yes," said Mr. Smith softly, and his eyes were far away. "I have always dreamed of stars."


	6. Fallen Angels

**Sorry this took so long! I hope I'm back on track, and I hope you enjoy it after the long wait!**

Fallen Angels

_Listen. Whatever happens, at least we're together_

_-Rory Williams_

Isabelle's first reaction to the red haired woman and her friend was to pull Max back and go running into the Institute, pretend she'd never spoken to the woman, and forget they'd ever met. However, the mention of Clary brought to mind her brother, and she felt that ache in her heart, the place that belonged to Jace. If there was any hope, if it was even a shred, she would go to the ends of the earth to get her brother back. Carefully, Isabelle pushed Max behind her, and Alec drew forward, closing the gap that Max would have run though. The little boy was forced to peek around Isabelle right side.

"You know Clary?" Isabelle asked carefully, giving the woman a challenging look.

"Clary Morgenstern, redhead, freckles, a bit on the short side?" Amy watched Isabelle's face stay firmly in its place. "Goes everywhere with that blond boy."

"Jace?" Max piped up, ignoring Isabelle and Alec's frustrated sighs.

Amy smiled victoriously. "Jace Lightwood and Clary Morgenstern, yeah we've seen them. I've talked to 'em."

Though Isabelle wanted to believe the woman, her instincts told her otherwise. There was something wrong about these people, some feeling on the back of her neck that made her hairs stand up. Whoever they were, whatever the reason, they didn't belong here. "You'll forgive us for not believing you."

"It's understandable, but, see, we've got nothing to lose and nothing to gain by telling you what we know, so, I think we might just tell you anyway." Amy shrugged playfully at Rory, who nodded in agreement. "Would you like to know?"

Isabelle shot Alec a quick look. He wanted to say no and turn and go, but the idea that someone might know about Jace was too tempting for him. "Just be quick about it; we're only allowed out for three hours a day, and we're running out of time as it is."

"Right, well, my name is Amy Pond, and this is my husband, Rory Williams, and we're, um…" Amy looked to Rory for help.

"We're visiting the city," Rory supplied. "We've come with a friend of ours, and usually, his transportation is pretty sturdy, but we got a little stuck here. Our friend, he took up a teaching position at a local school, and had a little run in with Jace and Clary."

"You expect us to believe that?" Alec asked incredulously. "That explains _nothing! _Somehow, some Mundanes just turn up in New York, and they can see through our charms, and they track down Jace and Clary, and they know we're all related? You're working for Valentine."

"No, we're not," said Amy, tossing her hair back. "It's a little complicated to explain, in fact, it's _a lot_ complicated to explain. Usually, when we travel, we don't go around telling people all about it, because, frankly, it's a little unbelievable-even for some people who spend their life hunting demons."

This drew Isabelle and Alec up; they hadn't shared their secret, so, how did this Amy and Rory know? "Demons aren't real," said Isabelle reasonably.

"Yeah, okay, and those knives are just for play," Amy snorted. "Listen, we know what you are, and we won't say it aloud- don't worry."

"We're just people like you," Alec said stiffly.

"No you're not, not even close," said Amy, and her eyes were glowing mischievously.

Rory nudged her a little. "Our life is a little more complicated than you think."

"Really?" Isabelle cocked a hip, unable to help herself. "I think, if you really knew Jace and Clary and us, you might not say those things. I think you have no idea who we are."

"I know the world isn't supposed to be this way," said Amy softly. "I know Valentine wasn't supposed to win the war, that you weren't supposed to be trapped her, and that Jace and Clary shouldn't be with Valentine."

"Well, as much as we want it, that's just how it is," Alec said simply. "We accept what we can't change."

"No, you don't get it." Amy leaned against the bars, her fingers curling around them and her face pressing closer. "_The world isn't supposed to be like this._"

"Well it is!" Isabelle snapped back. "This is what we got for trying to stop Valentine. Our family was torn apart and we're stuck in New York, waiting to hear if our parents are even alive."

Amy and Rory exchanged quick looks. "Listen to us," Rory urged. "You think this is just life, but it's not meant to be like this. Something went wrong, something happened that wasn't supposed to and Valentine won. He wasn't supposed to."

"You don't understand how life works apparently," Alec snorted. "Sometimes, things we don't like happen. When those things do happen, you just have to continue on."

"I'm going to try and explain this as best I can," Amy said slowly. "This war didn't end right, I know this, because I know how it was supposed to end. I know how it was supposed to end, because I've got a friend, the one we mentioned, and this friend isn't a normal man. He said the war was supposed to end with Valentine dying, so, something clearly went wrong."

"You're insane," Isabelle said firmly.

"Wait till I tell you the good part," laughed Amy.

"Which is?" asked Alec.

"So, this man, my friend, his name is the Doctor." Rory looked nervous all of a sudden, but Amy seemed unconcerned. "He's not exactly…_human_, the Doctor. In fact, he's-well, let's just say he's not from around here. He's kinda a history buff."

"What has history got to do with this?" pressed Alec.

Rory chuckled. "To the Doctor, everything is history."

"Remember how Rory said we were just visiting?" Amy asked, trying to judge if the children would take half of what she was about to say seriously. "We are only visiting, but not quite from another place. See, the Doctor, he's got this thing called a Tardis, and the Tardis can travel anywhere in space…or even anywhere in time."

As Amy and Rory expected, they were met with silence, probably skeptical. Isabelle raised an eyebrow and Alec pressed his lips together. Even Max had the expression of one who didn't quite believe. "So," Isabelle said, nodding her head. "you know a doctor who can travel through time? Yeah, yeah that makes perfect sense."

"Alright, mate, you're the one who goes around the world hunting down inter-dimensional parasites, because an angel tells you to," Rory said quickly. "Is it really so hard to swallow?"

"Time travel is impossible," Alec said flatly.

"For us, yes," agreed Amy. "The Doctor, though, isn't from around here. His people figured out how to travel through time ages ago. See, we weren't planning on even showing up here, but the Doctor took the Tardis too close to a white hole, some science stuff happened, and we ended up stuck here while the Tardis refueled, but now, she won't move. The Doctor figures that she won't go till we sort out this whole Valentine thing out."

"Sort it out?" Max piped up.

"Yeah, I _said_ Valentine wasn't supposed to win the war, and he wasn't! The Doctor said something went wrong in the flow of time and now Valentine is alive and in charge of the shadowhunters. Now, we're just stuck here, trying to fix it all."

"And you met Jace and Clary?" asked Isabelle sarcastically. "That's a bit a coincidence, isn't it?"

"Not with the Doctor," muttered Rory. "He's taken up a position at a school teaching math, and apparently Jace and Clary have been enrolled there by Valentine. We've been working on a way to get them away for a while now, but we need to figure out what went wrong in the first place."

"You're time travelers, who are teaching math on the side to make a quick buck while your time machine is busted?" Alec snorted. "I might believe in angels and demons, but this is ridiculous."

Amy's eyes narrowed. "Jace was really the son the Stephen and Celine Herondale, and when his mother committed suicide, Valentine and your old mentor, Hodge Starkweather, went and cut him from his mother's corpse because Valentine had been dosing Jace with angel blood. Valentine faked his own death and took Jace and moved to Wayland manor and raised him for ten years, faked his death again, and Jace ended up with you. Meanwhile, Valentine went and found his _real _son, Jonathan Christopher. Jonathan was dosed with demon blood, and it makes him more powerful and dangerous than any other shadowhunter alive. Clary, on the other hand, was also, unknowingly, dosed with angel blood and she can create new runes." When Amy paused to take a breath she saw that Alec, Isabelle, and Max were staring at her in shock. "Do you want to know any more?"

"How can you know that?" whispered Isabelle.

"Because we're from the future," answered Rory. "We know what was supposed to happen, but, apparently, something went wrong. Now, we're here, trying to set it all to rights. So you say you're parents aren't here?"

"They're in Idris," Isabelle murmured. "Valentine took them when they refused to drink from the Cup. I thought he was keeping Jace and Clary there…"

"No, as far as we know, they're in the city somewhere. They're going to school in some private, upscale place. The Doctor was planning on placing a tracker on Valentine soon so we could follow him home, and hopefully, get a lock on the location of Idris. If we can do that, the Tardis might be persuaded to take us there."

"No, technology doesn't work in Idris," Alec shook his head.

"The Doctor's does," said Amy with certainly. "We're just waiting to get a hold of Jace and Clary; they're still living with Valentine as far as we know."

"They're _living_ with him?" Alec asked, coming to life in a jolt. "You have to get them away from him. When Valentine was raising Jace he used to torture him, he'd beat him and brand him and whip him. He can't be living with him again!"

Amy and Rory shot a look at him. Rory said, "Valentine was pretty bad, huh?"

"He was awful to Jace, so the Angel only knows what he's doing now. Plus, he's got to train Clary." Isabelle was frantically twirling a hair around her finger. "He's a monster, and then there's Jonathan, and Jonathan hated Jace."

"We need to tell the Doctor," Amy said to Rory at once. "We can't keep waiting for them to come to us. The Doctor is going to have to get Jace and Clary alone and we're going to have to make a run for it."

"Clary and Jace won't trust us, and they're about as likely to believe the Doctor as Isabelle and Alec were," said Rory helplessly.

"Just tell them-just say…" Isabelle warbled off. Suddenly, she started pulling at the bracelet wrapped around her wrist fitfully. "Here, take this and show it to Jace. He'll know it's mine." Isabelle pushed her whip through the gap in the fence and into Amy's hand. "He was there when I got it for my birthday, he knows I never go anywhere without it. Show it to him."

Amy tucked the whip into her coat. "Good thinking. How long will you three be here?"

"Who knows?" Alec shrugged hopelessly. "If you really do manage to get Jace and Clary away from Valentine, he might take us to Idris to set a trap for them. Don't let Jace follow us."

"No need," Rory said quickly. "We'll be able to come get you in the Tardis. We just need a signal to track you with. Does anything you own give off radiation we can locate?"

Alec, Isabelle, and Max stared blankly back. Their education, though well rounded and detailed, was severely wanting where science was concerned. Radiation to them was a word that was attached to a vague meaning, like how the sun radiates energy or a demon might radiate darkness, but an object they owned that gave off radiation?

"Well, I mean, shadowhunters radiate their own kind of energy-"

"No, no, no," Amy shook her head, looking over the children quickly. "You know, energy radiation, like, electromagnetic radiation or something. Particles…" Amy's eyes landed on the necklace knotted around Isabelle's throat. "That should work perfectly. Can you wear that necklace at all times?"

"Yes," said Isabelle, confused.

"Okay, the Doctor should be able to track you down. That probably gives off its own radiation waves." Amy gave the three children one more long look, her eyes resting on little Max. "We'll come back for you, and we'll have Clary and Jace."

* * *

Jace was polishing off a piece of pizza, his feet propped up on the table, as he watched the television. On his lap was Clary's head, her hands curled around his upper thigh and his knee, her eyes were closed and her chest rising and falling in the deep troughs of sleep. Absently, he stroked her hair off her face and admired her delicate cheek bones and pink lips, the copper eyelashes that brushed her face. In her sleep, Clary murmured something, his name, and he grinned stupidly to himself.

"I'm here, Clary," he said back to her, taking her hand in his. "I'm here, don't be afraid." Clary turned over, tucking her face into the junction of Jace's thigh and hip. He marveled at her, marveled at her helplessness, marveled at her childishness in a world so hard as their own. He had grown up with no choice but to be strong, she had grown up softly and now, after being thrust into his, was still holding herself together. "You're amazing, Clary."

"Is the Long King still on?" she asked, caught in the confusion that clung to a person as they woke. "Did I miss Hakuna Matata?"

Jace chuckled. "Was that the song with the pig, gofer, and lion cub?"

"It's a warthog, Pumbaa, a meerkat , Timone, and Simba," Clary said sternly. "And, yes, that's the song."

"Ah, yes, I'm afraid so." Jace nodded to the screen. "Actually, the Lion King ended and another um-did you call it Disney?-movie came on. Now we're watching something about a genie."

"Aladdin," Clary corrected, laughing at Jace's crude description. "I can't believe I've been asleep that long. Is Father home yet?"

Jace shifted at the mention of Valentine. "No, he's still out. Hopefully he drove his car into an accident of something."

Clary laughed and sniffed the air. "Is there any pizza left?"

"Yeah, plenty, do you want me to get you a slice?" offered Jace. "There's even some bread left too."

"Yes, please," Clary murmured sweetly.

Jace kissed her and carefully detangled himself her and went to the kitchen. "It was rather generous of Valentine to get us pizza considering he didn't know our grades before he went. Let's hope the rest of the evening goes as well."

As Jace came back to the couch, Clary pulled him down into a very passionate kiss. They both had only a few words left, and it was easier for Clary to express herself that way anyway. Jace sank down, placing the pizza carefully on the table and joined Clary on the couch. He settled his weight on his forearms, being careful not to crush Clary. She was, for all her fire, still in a delicate state, and Jace knew lying on top of her wasn't going to be good idea. Beneath him, Clary squirmed.

Her hands lingered momentarily on the waist of Jace's jeans, but slowly, her fingers crept up under his shirt and traced the scared on his abdomen. Jace gasped suddenly, and, losing focus slightly, let his weight come down on his right knee, between Clary's knees. Under him, Clary laughed.

"Distracted?" she asked throatily.

Jace didn't reply, he didn't have to. Instead, he left his knee where it was and was able to lever himself up to her could kiss her throat. Not to be outdone, Jace ran his hands up under Clary's shirt, tweaking at her belly button and listening to her heart skip a few beats. He chuckled deep in his throat before returning his lips to hers.

The two remained that way for some time, Jace on top of Clary, his hands exploring her body, Clary fingers nervously toying with the hem of his jeans. Clary wanted to tuck her hands deeper, but she felt oddly out of place, like she was just a little girl, playing a game she didn't understand, and Jace was a grown man, looking more for a woman to love him than a girl. When their kiss broke, Clary took a rasping gasp.

"Jace I-"

"Get off my daughter," ordered a voice, and then Jace was tugged off Clary and tossed unceremoniously onto the floor. "I take you into my home, treat you like my son, and I find you trying to _violate _my daughter?"

"Father, please!" Clary begged, sitting up and quickly fixing her shirt. "Please, he wasn't doing anything wrong, I wanted him to!"

"My stepson is a womanizer and my daughter a whore," said Valentine bleakly, and then kicked Jace hard enough in the side to elicit the snap of a breaking bone. "Clarissa, you have some explaining to do."

"I-I don't know what you mean." Clary's eyes were on Jace. He was curled up in a ball to relieve some of the pain of the broken rib.

"I spoke with Mr. Smith, and I heard some interesting things…I _saw _some interesting things." Valentine looked Clary over up and down and then took her wrist and pulled her to her feet, shaking her like a rag doll. "_Your_ Mark was on his white board! Would you care to explain that?"

"My-my Mark? The silencing rune I made?" Clary was seeing tiny pinpricks of light when her father stopped shaking her. "He doesn't know."

"The where did he find it?" demanded Valentine, and then he took her hair and twisted it. "Answer me, you worthless little brat!"

"I don't know!" Clary shouted. "I swear on the Angel I didn't tell him."

"That's a bit rich, don't you think? Mr. Smith, a Mundane math teacher, just happens upon a rune that was only invented last week? Then I find it, written on his board?"

"I can't explain it!" Clary said sharply.

Jace had managed to pull himself off the ground and grabbed one of Valentine's arms, breaking his dangerous grip on Clary. "She doesn't know! She doesn't know!" he kept shouting over and over again. Valentine used his body weight and threw Jace off, and the smaller boy stumbled over the couch and crashed into the wall, his head banging off the side.

"Don't hurt him!" Clary cried, her fear of her father warring with her fear for Jace. "He didn't do anything wrong, he didn't tell Mr. Smith anything. He's been good!"

"I'm aware of that, Clarissa," said Valentine, dragging her away from the living room. "But, I've learned that you care very little for your own well-being, so I must resort to punishing him to elicit some response from you."

Jace rolled over on his side, his head spinning, and he saw the blurry image of Valentine tossing Clary down the hall to his study like she were a doll. He groaned, trying to put two thoughts together. _Valentine is angry…_This is true, he's furious. _He's mad at Clary…_Clary always makes her father angry. _When he's mad at Clary he takes her to his study…_The thoughts finally came together and Jace gave a strangled cry and straggled after the swirling image of Valentine. He reached the study door, but it was closed, locked, unmoving.

"Clary!" Jace cried, pounding his open hand on the door again and again. "Don't you hurt her, Valentine!"

"He's sounds agitated," commented Valentine casually. "Quite worried for you, actually. I'm rather pleased he loves you so much; it'll make it so much easier when you're both older. He'll be a good shadowhunter once he calms down a little. You'll help him with that."

Clary moaned in agony and strained her back. Her father had bound her ankles and wrists to the arms and legs of the chairs, and slowly, systematically, he was heating the flat edge of a knife and branding her skin. She watched red welts rise, on her arms, on her chest, on the back of her neck under her hair, on her legs once Valentine ripped her jeans off at the tops of her thighs. She squirmed under his hands, which we steady and sure.

"He's very dedicated," observed Valentine. "But then, Jace always was a serious boy. He'll come for you once I'm done, don't worry. You won't have to crawl back to your room. Now," said Valentine, kneeling down so he was on level with her, "why don't you explain why Mr. Smith knew your rune?"

"I've told you," panted Clary, "_I don't know_! He's just a stupid man and I didn't tell him anything. Why won't you believe me?"

Valentine pressed the flat of the knife to Clary's inner thigh and she screamed. She heard Jace echo her scream through the door. "It's too much a coincidence, and you and Jace are liars anyway. It seems only today I heard about some tutoring."

Clary's face paled. "We told him no," she said quickly. "We told Mr. Smith we just didn't have time. He believed us," she added.

"If he believed you then why bring it up to me?" pressed Valentine. "He mentioned it specifically to me at your conference. Now why would he do that if he believed you?"

"I don't know, but we said we were too busy." Clary's eyes were on the knife in his hand. "He doesn't know anything."

"I've told him I'll consider it," said Valentine to her surprise, and then lifted the knife to her face. "Are you that bad at math that you need private tutoring? Are you that pathetic?" He took Clary's chin and turned her face from side to side. "You're a disgrace." Clary was shuddering against her will, fear betraying her. Valentine placed the tip of the knife on her cheek bone and angled it to leave a small cut. Blood dribbled down her face. "You're afraid, Clarissa, and a shadowhunter should never be afraid. You're a worthless thing, completely, utterly worthless. It's not your fault; your mother raised you poorly, but even now, you refuse to learn."

Clary refused to let her lip tremble even though her father's words stung. She had never given much thought to what Valentine had said to her, but, the last few months had shown her that aside from Jace, she was completely alone; her mother had abandoned her and her friends were either dead or well beyond her reach. Clary had been, unknowingly, slipping into a depression, and hearing her father-her _own father_-telling her she was worthless was painful.

_Jace, Jace…please help me. _Clary's eyes moved to the door where it was now silent. Jace had stopped pounding on the door a few minutes ago and the comforting sound of him calling out for her was gone with it. _Don't leave me too_.

"I can't do anything with you," Valentine continued, and wiped the blood off her face. "This blood of yours, this is not mine. You're unwanted, Clarissa, completely unwanted. Your mother prefers me to you, your friends can't suffer your presence, if it weren't for Jace you would be utterly alone. Do you know that?" When Clary looked away, Valentine forced her to look back into his eyes. "Answer me, Clarissa. Do you know that no one wants you?"

"Jace wants me," Clary answered.

"Does he?" Valentine gave her a shrewd look. "Do you _really_ know that? He stays with you, yes, but does he love you? How can he, honestly, when loving you has gotten him nothing but pain and humiliation. If it weren't for you, he wouldn't be stuck in a Mundane school, he wouldn't be completely stripped of his rights, he wouldn't be beaten constantly, he might even be with the people he loves, with the Lightwoods. Do you think he wanted to give it all up just for you?"

Clary bit her lip. "He loves me."

"You don't know what that means," laughed Valentine. "You don't know the first thing about boys, your mother has told me that much, so why would Jace pick you? He could have any woman and you think he wants you that much? No, you're a burden, that's all." Clary stared at her shaking knees, but Valentine struck her face casually. "Say it."

She felt the command like a physical thing and knew Valentine was using the obedience rune on her back. "I-I'm a burden," she whispered.

"Yes, you are," said Valentine. "A burden to your parents and to your lover. Keep saying it, Clarissa, keep saying it till you run out of words. I want that to be your mantra from now on, I want you to know that."

Valentine rose and returned to sit behind his desk, paperwork spread out before him. Clary watched him go, her eyes pleading with him to let her go. When he sat, his grey eyes regarded her mercilessly. "You may begin."

Clary slumped in the chair and began to say, "I'm a burden" over and over. It seemed pointless to try and fight him when all he was asking for was words. She knew she ought to be grateful he wasn't hurting her, wasn't hurting Jace, but it still left her feeling empty on the inside. Valentine returned his focus to his work and remained silent for half an hour while Clary spoke herself senseless. When it was over, when all that was coming out of Clary's mouth was a desperate rasp, Valentine returned his attention to her.

"Good girl," murmured Valentine as he undid the bonds that held her. He tugged her to her feet and dragged her to the door to his study. "When you go to school tomorrow, you will tell everyone you had an accident. If I get a call about you, you won't go back to that school. I can't let them see the bruises you'll have then."

Clary stumbled out of the door with a startled cry, but before she even touched the floor, a gold shape shot out of the corner and swept her up. Though Clary tried to warn him of Valentine, the only sound that came out was a whistle of air. It didn't bother Jace though, he took one sweeping glance: the torn pants, the burns dotting her body, the cut on her cheek, her inability to speak, and then scooped her up to hold off the floor.

"Get her out of my sight, Jace," ordered Valentine, and his eyes met Clary in a silent challenge. "I don't want to see her-or you-until I pick you up from school tomorrow."

Jace bared his teeth in a lion's snarl. "Trust me, it won't be that hard."

Clary didn't make a sound as Jace carried her back to their room and settled her on the bed. She watched him guiltily as he carefully inspected her wounds. She averted her eyes when he sighed and gathered the bandages. She kept hearing again and again what her father had made her say, that she was a burden, and that's all she could think of as she let Jace tend to her.

"What did he do?" Jace asked as he wet a cotton ball and dabbed a burn. "Is this all, or is there more?" Clary shook her head helplessly, and then covered her face with her hands. A moment later, she felt Jace pull her wrists down and she was faced with his glowing, golden eyes.

"I heard what he said to you, Clary; I heard what you said, too." Jace kissed the tears off her eyes. "Don't you _ever_ believe that. I love you, I'll always love you, I'll love you no matter what Valentine does, no matter where we are, no matter what happens. Please just know that."


	7. The Doctor

The Doctor

_He's like fire and ice and rage. He's like the night, and the storm in the heart of the sun. He's ancient and forever. He burns at the center of time and he can see the turn of the universe. And... he's wonderful_

_-Tim Latimer _

At breakfast, Clary sat awkwardly at the table, trying to not to aggravate any of the cuts. Jace was in the kitchen, making toast and pouring bowls of cereal for the two, and his eyes never left Clary. It had been a hard night; Clary had stayed up late, sobbing into his shirt while he ran his hands through her hair, unable to rub her back. When she finally dozed off, Jace relaxed onto his back only to be woken a few hours later to her strange, strangled screams. He'd had to coax her into the fetal position, kissing her hair and cheeks. Neither of them had gotten much sleep.

"You should eat before we go," said Jace as he placed the bowl and plate down before her. "It'll make you feel better."

Clary stared at the bowl before her, feeling miserable and helpless. "What's the point, Jace? I'm better off dead."

Jace's face paled. "Don't you dare say that," he said softly but with conviction that turned Clary's eyes on him. "I told you-I told you all night-you're not worthless. You can't listen to Valentine because this is what he wants. He wants you to feel this way."

"But he's right," she whispered. "What do I do that's worth anything?"

"You love me," he said, dropping his eyes for a moment. "You're the first person, Clary, to love me like you do. Sure, the Lightwoods cared about me like a son, but you're more than that. You make me feel like I'm wanted."

"Because people want you," Clary argued, eyeing him jealously. Jace was a handsome, gifted, charming shadowhunter; of course he was wanted. "You're useful, at least. Valentine raised you and didn't hate the sight of you."

"You don't know that," laughed Jace darkly. "He wasn't exactly winning the best dad in the world award. As for being useful, you're more than I'll ever be; Clary, you can _create _new runes. That's impossible, but you do it. You're amazing." She stared into Jace's eyes and felt herself preparing an argument, but Jace silenced her. "But, most important, is that I need you. If you were gone, Clary, I'd be dead. I couldn't bear this place, this life, if you weren't a part of it. I need you Clary, because you're the only reason I have to live. You give me reason, a purpose. I'm worth it, aren't I?"

"Yes," Clary murmured into her breakfast after a moment. "Yes, you are."

After that, Jace refused to have any more conversation about it. He sat with Clary in the bathroom as she carefully applied make-up to cover the cut on her cheek. She looked helplessly on the burns on her chest and arms and chose a long-sleeved, scoop-necked shirt. Before they left, Clary made sure her hair hung to cover the burns on the back of her neck.

At school, Jace and Clary were silent. They didn't lift their eyes. They didn't participate in class. They could have been dead for all the world knew, but for their beating hearts. Clary caught a few eyes resting on her, and she panicked, thinking they might have spotted a burn. A few girls whispered how odd Clary was, and few boys thought that Jace had done it and considered reporting him.

When they finally came to math, Clary and Jace's now most hated subject, the Doctor was waiting for them with gleaming eyes. His eyes raced over Clary and Jace, and he felt his hearts beat a little oddly. There was certainly something wrong with them, and Clary kept tugging listlessly on her shirt collar. He guessed that whatever he or the other teachers had revealed about Jace and Clary's school work had not been met well at their home.

"Welcome students!" Mr. Smith cried, spreading his arms wide like it were a treat. "I hope your parents were all pleased." There was some grumbling among the students, but Jace and Clary remained stoically silent. Mr. Smith seemed to be, as always, blissfully unaware of any discontent. "Shall we get started on some math?" He, at least, sounded excited.

Mr. Smith set to writing on the board again, and Jace watched him, his eyes narrowed bitterly. He blamed Clary's punishment on the man, blamed him for being stupid enough to mention tutoring, blamed him for being so delightfully pleased with the world while he and Clary were condemned to hell. Part of Jace wanted to throttled the man, shake him still he understood.

_You mindless, stupid, bow-tie wearing Mundane, _thought Jace furiously. His eyes went irrevocably to Clary, who was seated, watching the board desperately. _You have no idea what you've done, what you're doing to us. I hate you. _

"Mr. Lightwood," Mr. Smith called, as if sensing his anger. "Would you care to answer the question on the board?"

_No_. "Yeah, sure," he shrugged and went to the board. Jace scribbled out an answer, hoping his calculations were correct.

Mr. Smith eyed the board. "Very nice." He winked at Jace, hoping to raise some sort of emotion from the boy, but Jace just stared back blankly. The Doctor swallowed back any more comments, and gestured Jace back to his seat; he was going to have act today.

"So, as you can see, Jace's calculations were correct and…" Mr. Smith continued to speak as the class became more and more catatonic. It wasn't that what he was saying was boring or pointless, it just seemed that way for a class full of high school students. He assigned problems and began his usual wander among the class, checking their work. He drew closer to where Jace and Clary were working.

"You two are being awfully quiet. Cat got your tongue?" he said with a winning smile, then his face dropped as he considered his words. "Well, not necessarily a cat, since they're not exactly known for eating tongues. Does make you wonder where the saying cropped up from, doesn't it? Cats eating tongues…" the Doctor made a strange face, sticking his tongue out and scrunching up his nose. Clary wanted to laugh, but her burns ignited pain down her sides, and she pressed her lips together. "Anyway, I was hoping to get a word with you two after class today. It'll be quick, just some concerns your father raised I thought might discuss with you."

"We really can't be late to English-"

"Don't worry about it," said the Doctor waving his hands rather madly. "I'll write you a pass to class. But this is actually very urgent, very important. It will only take a few minutes at most, just a few minutes."

Clary looked over at Jace wanly and said, "We'll stay. I'm sure my father will want to know anything about our grades." As she said it, Clary felt her heart drop; she wasn't sure how much more of her father's anger she could bear.

For the rest of class, Jace and Clary sat in silent misery. They had both assumed that whatever Mr. Smith had to say to them would get back to their father anyhow, and once it did, they wouldn't hear the end of it. Jace eyed Clary from his desk and decided that whatever happened next, no matter how bad it got, he was going to protect her. Clary was staring around the room with empty eyes, shaking a little bit against her will; she looked ready to fall apart. Jace knew she was strong, but Valentine's anger was breaking her.

As the lesson came to a close, the Doctor kept his eyes fixed on Jace and Clary. Part of him worried the children might simply go, and after Amy and Rory had returned from the Institute, their minds racing with what the Lightwoods had told them, the Doctor knew he couldn't let the shadowhunters return to Valentine. Students filed out as the bell rang, but, as requested Clary and Jace remained behind in their seats. Clary watched the others go dejectedly, wishing that her life could just go back to the way it was before Valentine had come. She slowly turned her eyes on Jace to find that he was staring anywhere but at Mr. Smith.

_It must be miserable when you're used to being the best, to suddenly be the worst, _mused Clary, thinking of Jace's life of training.

When the last straggler left, the Doctor snapped the door shut. He paused a moment, trying to think of the right way to introduce the frankly weird subject he was planning on to two disillusioned children. He rubbed his hands together contemplatively. "Right, so, we've got a lot to talk about, and not a lot of time. Alright, we're got a lot time, we've got all the time in world-the _universe_-but not here, not in this room. I don't store time in a classroom. You'll have to come with me." When the Doctor turned to see how they had taken it, he found Jace and Clary staring back at him blankly. He adjusted his bowtie, waiting for them to say something. "I'm being serious, you need to come with me; I can take you anywhere, but not while we're in here."

Jace, who found his voice first, seemed to only understand one thing the Doctor had said. "We need to go with you?" he asked, feeling like his mind was clouded.

"Yes, right now, actually, before the principal comes down here; he said he wanted to have a meeting with me over the ninth grade math classes." Mr. Smith smiled widely at them.

"Go with you?" repeated Clary faintly.

"Yes," said the Doctor. "Go, to leave, abscond, push off, push on, vamoose, and, my personal favorite, to take flight."

"We can't," said Clary after a beat. "We have to go home after school."

The Doctor leaned against the door, crossing his arms, and giving them a long look. Jace saw, for the first time, something in his eyes that made him shiver. He had felt from the first that Mr. Smith was not wholly human, but now, he felt it tenfold. His hairs stood on end, and though he didn't quite feel fear, he suspected it was only because he'd never seen Mr. Smith angry and was so confused by the man in the first place.

"Do you really _have _to go home?" asked Mr. Smith softly. "Do you want to go home to Valentine? I get the impression from that man that he's not going to be winning Father of the Year anytime soon."

"He's very good to us," Clary said as firmly as she could, considering the repercussions if she failed him.

"Good to you?" asked Mr. Smith sharply, and he pulled himself from the wall with that same chaotic energy he'd had on the first day of class. "Is his goodness to blame for your nervousness, your silence, those shadows under your eyes?"

"We're fine," Jace repeated, and he put all the strength he could into his voice.

"I'm not a fool," Mr. Smith said darkly, considering his next words. "I know Valentine isn't your father Jace, he's not even your father, Clary, not in any real sense. You'd probably prefer Luke."

Clary felt the color drain from her face, her mouth moving against her will. "L-Luke? I don't know any Luke, you've got me confused for another student-"

"Luke, you know, the guy with the fur problem about once a month?" Mr. Smith waved his hand over his own body. "I can only imagine why Valentine doesn't want him around, seeing as your mom practically lived with him. I get the feeling Valentine is the jealous type."

"Stop this," Clary said, terror gripping her. If Mr. Smith knew this, it was going to get back to her father, and her father would blame her and he would punish her. "Stop talking."

"But then, Valentine always hated those-what did he call them?-Downworlders." Mr. Smith had joined them at their desks, and his eyes were far away on another memory. I suppose he's had most of them executed since he summoned the angel?"

"Stop talking!" Jace snarled suddenly, lunging to his feet. Mr. Smith started when Jace turned on him, his eyes widening and taking a nervous step back. "Just stop talking. You're not helping _anyone _with it!"

"I'm trying to help you if you'll let me," said Mr. Smith gently, holding up his hands. "Let me help you, just come with me and I can fix everything."

"You'll fix nothing!" Jace spat, griping Clary's shoulders to calm himself. "We don't want your help, we don't need it. All you're doing is making things so much worse."

"I can make everything better, just listen to me-"

"Stop, stop, stop!" Clary cried, jumping to her feet. "I don't know who you are, I don't know how you know what you know, but just stop. Valentine will be furious if he ever knew. We won't say anything to him, I swear, but you have to leave us alone."

"Listen to me!" Mr. Smith ordered, and though his voice was soft, it was hard as steel. "I can help you, I can make everything better, but you have to trust me a little. I know it sounds impossible, I know you think I'm lying, or you think I'm some crazy Downworlder or something, but I'm not. I'm much better than anything you could possible begin to imagine."

Clary laughed hoarsely. "There's nothing you can do."

"Isabelle says otherwise," said Mr. Smith simply, and carefully, he reached into his tweed coat and removed the golden whip. It was curled up in its bracelet form, but Jace, who had seen that whip for years, recognized it at once. He felt his mouth hang open and he quickly snapped it shut.

"What did you do to her?" he hissed, and then drew Clary back into his arms. "Are you working for Valentine? Is this just some sick test-"

"I'm not working for Valentine," said Mr. Smith, looking thoroughly disappointed. "Trust me, he wouldn't want a man like me in his retinue. I'm not what you would call…human." He shrugged as if the entire concept of being human were overrated.

"You're a Downworlder?" Clary asked. "You've got some nerve, being a teacher to Valentine's children."

"I'm not one of those either," said Mr. Smith, and his eyes dropped like a guilty child.

Jace had raised his eyebrow, but the sight of Isabelle's most prized possession in Mr. Smith's hand urged him on. "Really, so what are you?"

"Well, I mean to say, it's a little complicated." Mr. Smith cupped his hands together, bending over a little, and walking around in a possessed manor. Clary was reminded of the books she'd read of Sherlock Holmes; of his pacing manner and his self-possessed wisdom. "See, I'm not exactly from this…planet, technically," he said quickly. "I'm more of a visitor, a guest, a frequent caller, if you will."

"You're not from this planet?" Clary said, unable to stop the sarcasm that tainted her tone. "Yes, that makes sense. An alien from another planet has landed in New York, completely unnoticed, and he happens to be a calculus teacher as well. Gosh, I've been silly."

"Well, you know," said Mr. Smith, "you're the one who thinks an angel arrived on this planet, mixed his blood in a cup with yours, and somehow, made a new species. That sounds about as far-fetched as me being from another planet."

"You really think we're going to believe this?" Jace said, and a smirk curled his lips.

"No, not really," agreed Mr. Smith, suddenly happy. "Most people don't till I give 'em a spin on my Tardis, which, consequently, I'm more than willing to do for you. However, that involves us getting _on_ the Tardis, which, as I've said, we need to do soon. Time is of the essence here, well, when I say here, I mean this literal place," he gestured down at the ground as if he couldn't help but move, like energy was bursting from him. "Once we get on the Tardis, things will be different."

Clary blinked and shook her head. "What are you talking about?"

"My Tardis." Mr. Smith spun about to face her, his eyes glittering and he took off speaking faster than Clary or Jace could really understand. "She's beautiful, wonderful, the most powerful ship in the universe! The engine is a perpetual supernova-_The Eye of Harmony_, allowing her to travel through time and space at will. She's infinitely huge on the inside, got everything you could possibly want, I promise you that, and if she doesn't have it, she'll make it. Libraries, pools, tennis courts, toy rooms, bedrooms, the possibilities are endless. Did I mention I time travel?" He jumped as if he'd said something that had even surprised him. Jace's face had finally given way to confusion and Clary's mouth was hanging open. "I do, I travel through time, I'm a Time Lord." He seemed embarrassed by this.

"You're mad," said Jace weakly. "You don't work for Valentine, because you're mad."

"Well, maybe," admitted Mr. Smith. "Madness and brilliance have always seemed to go hand-in-hand as far I've seen. Do you think one negates the other?"

"Where did you get the whip from?" demanded Jace, turning the subject before they lost track. "What did you do to Isabelle?"

"I didn't do anything to her. Amy brought this to me, said Isabelle told me to show it to you so you would know she was behind this." When Jace continued to glare, Mr. Smith sighed. "Amy, you know, the red haired woman you met who said she traveled with me?"

"Where did she meet Isabelle then?"

"At the Institute," shrugged Mr. Smith, and then he pressed his face against the door, peeking out a crack in it. "Alright, the principal is almost here, and we haven't got time for this. Please, just trust me. I'll help you, I'll make everything all right." He saw the guarded expressions on their faces and ran his hands through his hair and spoke slowly. "I'll protect you from Valentine, I swear I can. No matter how powerful you think he is, no matter how much control he seems to have, I _swear _I can take you places he can never reach. I can make sure you never have to see him again."

"But you can't," Clary whispered. "He can track us, he can order us back to him, he'll hunt us down. There is nowhere, no way, you can help us. It's impossible."

Mr. Smith's face fell and, to Jace, he seemed suddenly immeasurably sad. He rushed over to Clary, taking her hands in his, and Clary felt a strange rush of energy and strength burst through her. "You can trust me to help. I am and always will be the optimist. The hoper of far-flung hopes. The dreamer of improbable dreams." He brushed his thumb over Clary's cheek and she felt like a little girl again, looking up into the eyes of Luke. "Trust me to help you."

"Okay," Clary whispered, hoping beyond all hope what Mr. Smith was saying was true.

As Mr. Smith led Jace and Clary away from the school, he was speaking to them, muttering really. It was a steady stream of words that didn't really make much sense to the two shadowhunters, he kept going on about _the_ _Tardis_, and_ the_ _time vortex, _and _paradoxes_. Once in a while, he would turn around and tell Clary he was going to fix everything, or tell Jace that he was going to be amazed beyond his wildest dreams. As they went, they earned a few confused stares, mostly because Mr. Smith was dressed so oddly and Jace and Clary looked so forlorn. Then, Mr. Smith rounded a corner to an alley and spun around, throwing his arms up like a conductor.

"Isn't she beautiful!" he cried, smiling widely at the two. When they looked back at him with empty eyes, his face fell a little. "I mean, sure, she doesn't look like much from the outside, but wait till you look inside-"

"That's a phone box," Jace said, bored and tired. "You've led us to a blue phone box down a secluded, questionable alley. Clary, he's insane."

Clary stared at the blue phone box and decided at once that she liked it. Maybe it was because it looked so sweet, so perfectly out of place, but Clary was reminded of London in the 60's for some reason, and it was a balm on her recent hectic life. _Besides, that's a pretty blue, _she thought. "How can you travel through time and space with a married couple in a small, blue box? How do you fit?"

"Well, it's hard to explain when you don't understand physics," shrugged Mr. Smith.

"Why is there a light on top?" asked Clary, staring at the small light. "Do you change the bulb often?"

Mr. Smith burst into laughter. "You're not the first red-head to ask me that." He wiped his eyes and then gestured to the blue box. "Come along, shadowhunters, come along. Once we're inside, everything will be fine."

"Mr. Smith," Jace said, his voice taut as a wire, "we can't all fit in there."

"Please, Jace, my name is not Mr. Smith. You can call me the Doctor."

* * *

When the Doctor threw open the doors to the Tardis, Clary and Jace felt a rush of wind blow back their hair, and they heard the Doctor's footsteps as they echoed off a metal floor. Gradually, the shock of what they were staring at wore off long enough for them to take a step over the threshold of the Tardis and into the control room. The Doctor was running around a huge tower that, to Clary and Jace, seemed to be alive and glowing. As soon as they were in the Tardis proper, the doors swung shut with a snap and Clary stumbled away from them, Jace catching her. Their eyes left the closed, oddly wooden, doors and traveled up the wall. They tried to see the ceiling, but it seemed to vanish into impenetrable darkness. Clary felt dizzy, so she looked down at her feet only to see the grating, and below that, a strange blue light. Clary's heart started to pound and she saw across the room, a staircase that led off down a hall with the same blue light.

"It's huge," Clary whispered weakly against Jace's chest. "Jace, it's huge."

"It's impossible," Jace breathed back. "_This_ is impossible. You can't have a dimension just locked up inside another one. You can't."

"What do you think?" cried the Doctor. "Amazing, isn't it? Please, feel free to make yourselves at home. Hang your coats up." He pointed to the coat hanger behind them

Jace whipped around to the coat hanger and stared. It was the placement of this perfectly normal, perfectly mundane, object in the middle of a time machine that finally got to him. He'd seen too much in such a short time, suffered too much lately; his nerves were frayed. When Jace turned back to the Doctor he knew he was looking at something that wasn't human, something that wasn't even from this world, and that scared him more than cared to admit. This thing was capable of fitting another dimension in a box, he could travel through time and space. He seemed to be infinitely capable, infinitely dangerous.

"You're not human," Jace accused.

"I told you I wasn't," laughed the Doctor, and he jumped back down to meet them. "I find being human to be slightly overrated, don't you think? I hope you believe me now, now that you're safe and sound in the Tardis."

"We're not safe," Clary said, narrowing her eyes at the Doctor. She jerked back her sleeve to reveal her wrist and the Mark her father had placed there. "My father did this, it's a tracking rune. He'll hunt us down the moment he doesn't see us after school."

The Doctor gently turned her wrist over, his ageless eyes glancing over the Mark. "Impossible," he announced. "You're in the Tardis now, in a different dimension. The interior of the Tardis is in a state known as _temporal grace_. Technically, anything inside the Tardis doesn't exist. _You _don't exist while in here, so how can Valentine find you?" He was smiling again, and Clary hoped that same unbelievable hope. "Besides, nothing gets through those doors, nothing. No shadowhunter, no demon, no angel, and trust me, they've all tried before." Something in the way his voice changed told Jace he was speaking the truth. "Come along, I'll show you around."

Jace placed his palm on the small of Clary's back and the other on her shoulder and began to lead her after the Doctor. Their eyes strayed from the Doctor, glancing off the hard metal interior, and they thought how cold and empty the Tardis was, ignoring the life that seemed to be thrumming through it. Clary slowly turned her eyes back on the Doctor and he was fiddling with knobs, flashing lights, pushing buttons on the counsel. When he saw her looking, the Doctor suddenly smiled.

"You're inside the largest, most-powerful ship in the universe. She's a bit picky, but she's been around for a long time, and she always seems to get me where I need to be."

"It's so big," breathed Clary again.

"How do you trap another dimension within the other?" asked Jace starkly.

"The Tardis is _dimensionally transcendental_, this means the interior is a separate dimension from the exterior. It's a little complicated to explain; Time Lords were the only ones as far as I know to understand transdimensional engineering. But, that's how it's done," he shrugged, as if the entire idea of dimensions in dimensions were mundane. "I can show you to your rooms if you like, or the library, or maybe the pool or-"

Clary had been listening to the Doctor and she felt her heart start to beat faster. Even though he was talking, even though he sounded reasonable and pleased, Clary thought that it was all too much. She tossed Jace's hands off and she rounded on the Doctor.

"Stop talking, just stop talking!" Jace tried to grab her, terrified she was going to get herself thrown out. "This doesn't make any sense, everything you're saying-it's crazy. It can't happen, none of this is real!"

"Well, I said that," nodded the Doctor.

"Then why are you lying?" Clary demanded. "Why is all of this a lie? This place can't be real, I'm not safe. _We're_ not safe." She turned on Jace just as he managed to pull her back. "Stop it, Jace. You know I'm right, you know it's not real." She sounded desperate, almost crazed.

Jace's eyes darted up to the Doctor, and he was surprised to see the man was looking confused-not angry. "Clary, it's real, it's all real, just a little confusing…"

"No, it can't be real," Clary shook her head determinedly. "You said it yourself!"

"Help me," Jace hissed at the Doctor, who was still looking anxious and confused.

"What am I supposed to do?" he said, his voice adorably like a young boy's. He waved his hands at Jace in a shooing gesture. "You're her _boyfriend_, you do something!"

Clary screamed again and tried to worm her way out of Jace's arms when a door slammed above them. Amy and Rory were watching the struggle and Amy rolled her eyes. "Never leave the boys alone." She tripped down the stairs easily and came over to where Jace was holding Clary. She helped Jace lead Clary to a seat and sat her down, enfolding the girl in her arms. "It's okay, Clary," she cooed. "Try to breathe, try to focus on breathing. I know it all seems crazy, you should have seen me the first time on the Tardis…" Amy continued to speak softly to Clary, and Jace was impressed to see that Clary was gradually relaxing into her arms.

Maybe it was the patient rhythms of her voice, maybe it was that Clary had gone so long without an adult woman in her life, but she broke down into sobs in Amy's arms. Clary felt, for the first time in months, that she was being cared for, maybe even loved. Amy was holding her, enjoying the feeling of a small, warm body in her arms, and she rubbed her back comfortingly.

"Who are you?" Jace asked sharply, eyeing Rory. He didn't see much to the man, just a nervous looking Mundane. "You don't look like much of a time traveler to me."

"I'm Amy's husband," Rory said, and, though Jace felt Rory's eyes on him, he didn't know Rory was looking at the way Jace held himself. He looked wary, like an animal that was cornered. "I'm Head of Nursing at a hospital."

"A nurse, a model, and an alien," Jace said darkly. "This makes sense."

"You get used to it after a while," Rory said in an offhand sort of way. "I thought it was all bit crazy at first, you should have seen what it was like first time out. Let me tell you, space fish…" Jace gave him a strange look but then turned his attention back on Clary.

Clary was still sobbing, and Amy could feel her body shaking in her arms. She tried to calm the girl down, rubbing her back. As her hand made small circles on her back, Amy pushed Clary's shirt up, and her fingers brushed over scared tissue. Amy's eyes widened in shock and Clary stopped crying at once, her back straightening and her gaze shifting up.

"Clary, what is this?" Amy asked, and Jace's heart skipped a beat. "Are you hurt?"

Rory had moved at once to Amy's side, but Clary jerked herself out of Amy's arms. "It's nothing, it's just a scratch." Her eyes went to Jace, imploring.

"Clary, you have scars all over your back," Amy said, pushing the hair out of the girl's face. "What happened to you? Who did this?"

Amy's concern must have alerted the Doctor, who had joined them. His face, for once, was looking uncharacteristically serious, his eyes dark with age and something else. "It's nothing," Jace said again.

Rory was trying to take a closer look at Clary's back, but Jace's sudden outburst had drawn his attention. "Who did this? This isn't accidental."

Jace pressed his lips together. "We have to go," he said swiftly. "Clary and I need to go back. We're in enough trouble as is."

"You're not going back," said the Doctor, and his voice was stern. More stern than even Valentine had ever sounded. "I brought you here to protect you-apparently from this."

Clary was looking panicked, her eyes racing between Jace and the Doctor, her hands clutching desperately at her shirt. "Jace is right," she said weakly, but she was shaking under the Doctor's cold look and Amy's sympathetic eyes.

"Let us help you," Rory said gently, rubbing her shoulder. His eyes moved over to Jace who was pale and nervous. "Let us help both of you."


	8. Fury of a Timelord

**Hey everyone! So, starting on Monday, I'm spending a month doing some research, and I'll be out in poor internet land. I'm not sure how often I'll be able to connect, so my next update might be a little late. **

Fury of the Timelord 

_That was the worst thing…the fury of the Timelord…and then we discovered why. Why this Doctor, who had fought with gods and demons, why he had run away from us and hidden. He was being kind._

_-Son of Mine_

Valentine stood alone, a little ways away from the school, looking like nothing to much as a casual businessman waiting for his children. A few of the mothers who had come for students were watching him, smiling faintly whenever his grey eyes turned their way. To an ordinary person, Valentine was handsome with a self-contained grace and force of presence that marked him out. None of them knew that he wasn't human, none of them knew he was a cruel, often sadistic, father who was even now waiting for the children he abused, and none of them knew how little he thought of them.

The bell rang and Valentine watched as a number of children emerged from the school. Somewhere in the back of his mind, Valentine took a little pride in the knowledge that he made the world safe for these people. However, it was clouded out by the irritating thought that his children were late arriving. He had thought after his little display with Clary, they might be a little more willing to obey, or at least, a little more scared. Instead, he got this.

_She's her mother's daughter, _he thought bitterly. _So rebellious and hard-headed…not nearly a proper shadowhunter. I'm going to have to work on her, it'll take a while, and her attitude…it's rubbing off on Jace. He's getting worse, I'll have to have Jonathan put him back in his place. _It troubled Valentine that his grip on his children seemed so tenuous, and he liked to deal with things that troubled him. _So, where are they? _

Still, the children poured out of the school, and still, there was no sign of his daughter and Jace. Families drove away, children walked past in groups, teachers even left the building, and still, Clary and Jace were nowhere to be seen. Valentine rolled his shoulders thinking, _I'm going to make them regret this._ And then he entered the school, eyes dark, and went to the administrative office, hoping a secretary might know where they were.

When the secretary spotted the tall, broad-shouldered man entering the office, a wave of delight passed through her. Handsome, elegant, clearly well-off, he was the prime example of what a father should be, and besides, she liked children. "Hello, can I help you with something?"

Valentine smiled wanly. "Just looking for my children, Clarissa Morgenstern and Jace Lightwood."

"Ah," said the woman, recognizing the names. She typed into her computer and waited while registrars for the day popped up. "It seems both Clarissa and Jace were present in all their classes today, except for English. Last period." She glanced up to see how the man would take it, but his face was composed, not showing even a hint of surprise. "If they weren't leaving early today, they may have gotten a pass to skip last hour and have a free study period instead."

"Of course," murmured Valentine. "A thought…they were offered some extra tutoring by their math teacher, Mr. Smith. Perhaps he knows where they are?"

The secretary smiled widely. "Mr. Smith? I'll contact him," she said as she dialed the number to his classroom. "He's such a bright young man, and so polite; I heard he graduated from Oxford." Valentine heard the dial tone continue, but no answer, and somewhere, a small alarm went off. "Hmm," hummed the secretary. "Let me try his personal extension, the one he left at the front desk. He might be in the library." She dialed again, and this time, after four rings, a message played. She frowned. "It seems Mr. Smith isn't answering his phone."

"A forgetful man, no doubt," Valentine said, and his suspicions grew.

"You can say that again," came a gruff voice from behind them. It was the principal, and he was looking dark and moody. "Mr. Smith and I had a meeting planned for today for fifth period; I get to his classroom, and it's completely empty, lights off and all. His class had been cued up for fifteen minutes in the hall. Where the hell has the man gone?"

_I think I know_, Valentine thought to himself, and he felt his hands constrict. At just that moment, though, his phone rang and he snapped it open. "Hello?"

"Father, something strange just happened. I was using a mirror to track down Jace and Clary, but no picture formed. It just showed darkness." Jonathan paused, giving the mirror a good bang on the table. "What's going on?"

"Nothing, I'll be home soon," he said tersely, and then turned back to the principal and secretary. "That was my son, and it seems he came by and picked them up early. Clarissa wasn't feeling well. Thank you," he said by way of dismissal and left the school in rage.

_Jace and Clary gone, Mr. Smith vanished, and Jonathan unable to track them down? _His thoughts raced back to Mr. Smith; the man had seemed like an ordinary Mundane with a few strange exceptions in mannerisms, but that was nothing. _Whoever you are, Mr. Smith, I'll track you down. _

Valentine removed his phone from his pocket and dialed the number of the phone Jace and Clary were allowed you use. It rang, it rang again and again and again, but still, no one answered. Valentine felt a muscle work in his jaw as it continued ringing, and he knew they were running. _Running, running just like Jocelyn did, but it won't buy them fifteen years. _When the message came, Valentine growled into the phone.

Caught in the grip of a panic attack, Amy and Rory helped Jace to escort Clary away from the counsel room and into a bedroom. Jace was concerned for Clary, but that didn't stop him from staring around him in shock as he passed down hall after hall filled with strange blue lights. When they finally came to a door, it slid open and revealed a large room. Clary was staring blankly at the room, still uncomprehending, still in shock by how so much could fit in somewhere so small. Jace felt her go slack in his arms.

"Why don't we get you into bed?" Amy offered Clary, helping her to wander across the bedroom's carpeted floor and onto the bed. Amy started throwing open drawers, digging around for a bed shirt and shorts Clary could wear. She continued up a steady stream of conversation to keep Clary from reverting back into her crazed muttering.

Rory was hanging back at the door by Jace, his eyes slid sideways to view Jace. "Valentine is her father," he said softly.

"Yes," Jace replied just as quietly. "He has an odd way to go about raising his children."

"He raised you too, didn't he?" asked Rory with a straight face.

"Yes, but that was a long time ago," mused Jace. "I was just a little boy back then. This is different, this is his daughter, and she's not a little girl he can scare into obeying him. Instead, he hurts her." Rory nodded faintly and Jace looked him over. "Do you have children?"

Rory gave him a twisted smile. "Yes, I did. A daughter."

Jace picked up on the past tense. He was used to hearing about parents losing children and children losing parents. "What happened to her?"

"It's a bit confusing, to be completely honest." He saw Jace's curious eyes and sighed. "Melody was taken from Amy and I when she was born by a religious group called The Silence, whose goal was to kill the Doctor. They raised her to be a soldier, and four years from now, she killed him."

Jace blinked once. "She killed him…four years from _now_?"

Rory grinned a little. "This is all in the past for us, you see? It's already happened. Melody-River, that's what she goes by-killed the Doctor in 2011 for the Silence and was later imprisoned in Stormcage for murdering him."

"But the Doctor is alive," Jace pointed out, his mind trying to comprehend what Rory had said.

"Yes," agreed Rory. "Well, the Doctor is rather brilliant at escaping; he faked his own death, on a _universal _scale, and erased himself from the history of the universe. Then, he just went on living."

Jace, who had spent most of his life with the knowledge of his imminent death, found the concept of evading it impossible. "What happened to your daughter, is she still in prison?"

At this, Rory laughed aloud. "Remember I told you the Doctor erased himself from the history of the universe? Well, how could River be imprisoned for murdering a man who never existed?"

"Why would the Doctor do that for the woman who murdered him?" Jace asked, and he realized there was much more going on inside that man's head than he'd ever even begun to think.

"Well, it does make it rather difficult for the Doctor to visit his wife when she's in prison." Rory shrugged helplessly at Jace's open-mouthed stare. "Yeah, they're married."

"He's insane," Jace breathed.

"I've been saying _that_ since I met him," Rory said. "But, he's a good man, and that's what most important. You trust him, don't you, Jace?"

Jace frowned and looked away. "I guess. He certainly could have harmed us by now if it were his intention. If he can help us escape Valentine? That's a different story."

"He can," said Rory with certainty. "That man, he's done things-impossible things. I've seen him fight demons and angels, bring the dead back to life, turn entire armies with just the mention of his name, and he'll help you too."

Jace turned back to Clary and said darkly, "I've never known a person to do those things for no reason but that he can. I think the Doctor should consider the situation before he decides to challenge my father."

Rory chuckled. "Jace, you have no idea what the Doctor is capable of. But, for now, let's just work on getting Clary and you back in shape. Would you mind taking your shirt off and showing me your back?"

"I'm fine," said Jace sharply, turning about to face him. "It's Clary who needs help-"

"I doubt you're fine, since you said yourself, Valentine raised you. Besides, I can't do anything for Clary until she calms down. I'll have to give her a sedative just to get her to relax; I really don't want her having a heart attack."

"Then take care of her!" Jace demanded, pointing furiously at Clary who was now tucked into bed.

"Jace, I'd rather make sure you're in order while I can." Rory reached out for Jace arm and tugged his sleeve; Jace, in a panic, jerked back and his sleeve tore. Rory inspected Jace's arm with an unimpressed look. "Would you care to try and explain these marks, or do you just want to take the rest of your shirt off?"

Jace flushed pink and pressed his lips into a line. "Please," he said, and though his voice was even, Rory knew it was closest Jace would ever come to pleading. "Just take care of Clary first. If you make her alright, I'll do whatever you want, but I just want Clary to be alright."

Rory placed his hands on his hips, every fiber of his nursing self wanting to attend Jace first, but he saw the determination in Jace's eyes. "I'll give her a sedative and check her over, but please, let me fix you up first."

Jace nodded and he and Rory went to the bed where Amy was soothing the hair off Clary's face and humming. When she saw Jace, Clary's eyes widened. "Jace, you need to call my father, you need to tell him we're going home, you need to tell him we're sorry-"

"Clary, it's going to be okay," he said softly, trying to copy the way Amy had been stroking her. It seemed, though, it was simply something mothers knew how to do because Clary fidgeted and Amy took over again. "I'm going to stay with you, I'll be right here with you when you wake up. You should sleep now."

"He's going to be furious, Jace, and I can't-I can't face him again." Clary shuddered just as Rory came up behind them, a needle in his hand. Clary's eyes saw the point and she thought of her father slicing her toes. She started to thrash. "No! Not that, not that again."

Rory's eyes got wide, but he glanced to Jace who steadied Clary as she struggled. Amy tried to calm the girl down, but she refused Amy's touch, and even tried to throw Jace off. Rory moved quickly, inserting the needle into her arm and watching as the liquid drained into her body. Clary, lying helpless on the bed, felt something cold seep into her blood, weighting her arm down. She looked up at Jace, mouthing wordlessly and slumped back as the drug took effect. Jace smiled weakly down at her, but as Clary slipped off, Jace felt oddly abandoned and he suddenly wanted her back.

_You're not alone,_ he told himself firmly. _Clary is still here, she's still here on this spaceship with you, you're on a spaceship…_ It hit Jace again and he glanced around himself uncertainly. Rory was checking Clary's pulse and Amy was petting her hair and looking over at Jace with curious eyes.

"She's going to be okay, Jace," Amy said firmly, and then she reached out and took his hand in hers. Jace, who was even less accustomed to a mother's gesture, jumped. "Rory and the Doctor will take care of everything. Why don't you change into pajamas or something more comfortable? There's got to be some in this place somewhere." Amy squeezed his hand again and got up, rummaging through another drawer while Jace watched bemused. She found a pair of sweats and a blue tank, and, for some odd reason, a tie. She tossed the tie aside with a raised eyebrow. "Never know what you find around here. Throw these on and let Rory take a look over you."

Jace held the clothes out before him and stared back at her unhelpfully. "Can't I just sleep?"

"Better now than later," Amy shrugged helplessly.

Jace hated when people worried over him-really worried. It was one thing for him to get attention from Isabelle or Alec when he had a broken bone or a nasty bruise, that was his own recklessness that earned him those. He'd made a point of glossing over any abuse he'd suffered at Valentine's hands as a boy as he thought it made him seem weak or helpless. Now was the very same situation: he, hurt and helpless to his situation, them, fussing over the state he was in.

As he carefully peeled his shirt off his back, he heard Amy's intake of breath, but that was all. Jace knew what he must have looked like: bruises, broken ribs, and jagged whip lashes; nervously, he rubbed his feet together, hoping Rory wouldn't notice the slices there. Rory felt a surge of anger pass through him when he saw extent of the damage done to the boy by his own father, but sensed Jace's discomfort.

"Lie down," Rory ordered gently, and began to examine the wounds. The whole while, Jace held his face in an expression of impassive boredom, but beneath his mask, he felt oddly comforted to have Amy smiling encouragingly down at him. Once Rory had finished his inspection, he pulled Jace up. "I'm going to set your ribs and give you something for the pain. The bruises should go away on their own, but as for those cuts…where did they come from?"

Jace turned his face away to look down at Clary. "Electrum wire whip," he murmured, just audible. "It's what we use to cut demons with, but it can leave some nasty lashes on humans."

"No kidding," Rory whistled. "Is there anywhere else I need to check over?"

"No, none," said Jace, but just a bit too quickly; he saw Rory and Amy's skeptical look.

"Jace, if you're hurt, I need to know. If there's an open wound, you could get an infection, and if there's a broken bone, it could set wrong-"

"I know!" snapped Jace, rolling his eyes, but then, reluctantly, he propped up his feet on the bed. "There's some cuts between the toes."

Rory took Jace's feet and prodded gently at the cuts; Jace flinched against his will when he felt the still smarting nerve ends. "I might have to stitch these closed, they're so deep. Does Clary have the same cuts too?"

"Hers are deeper," Jace said darkly. "If you're going to sew them, now seems the opportune moment, no?"

"After yours, Jace," was all Rory said.

It took a while for Rory to disinfect and close up the slices, but Jace remained silent and calm throughout the ordeal. Afterward, Rory had Jace lie on his side so he could feel around for the brake in his ribs and set the bones together. Amy held Jace's hand as Rory set the bones and he convulsed when the bone popped into place. When he was done, Rory wrapped Jace's torso in gauze and gave him powerful painkillers.

"Will you take care of Clary now?" pressed Jace. "She's in worse shape than me; Valentine was horrible to her."

Rory looked wary of staring anew on another victim, but he nodded faintly, saying, "You should lie down, you look half dead. Just go ahead, lie down next to Clary. You lived together before anyway," he shrugged, pointing to the empty half of the bed and then turned his attention on Clary.

Amy came around to Jace's side and sat down next to him as Rory started on Clary. "Not too horrible, I guess?"

"I don't like when people treat me like a child," said Jace, eyeing Amy.

"I understand." Amy shook her head. "It's kinda tough on young people, especially when they just want to keep going. But there's always that one adult who holds you back."

"Your parents must have been fun," Jace laughed.

"I didn't always have parents," Amy said in distant voice. "See, when I was a girl, I lived in this huge house, but I lived there with just my aunt. It turned out there was a crack in the universe, and it was pulling things into it, and once you got pulled in, you didn't exist. That's what happened to my parents."

Jace had rolled over and was staring up at Amy, who was mindlessly, rubbing Jace's shoulder. "Your parents didn't exist? Did you ever get them back?"

"The Doctor got them back. He closed all the cracks in the universe and-and restarted time, restarted the entire _universe,_ and then I had parents all over again."

"So, the Doctor faked his own death, erased himself from the history of the universe, and restarted the universe." Jace shook his head. "Anything else to add to this man's fame?"

Amy laughed. "Well, he didn't do it in that order. He fought in a war once too, the last Time War, but he never talks about it."

"That man in a bowtie was in a war?" Jace couldn't hide his sarcasm.

"Yes," nodded Amy, and she looked away painfully. "All his people died in that war, so he doesn't like to talk about it much. Maybe if you ask him, he'll let you in, since you and he are both soldiers."

"He just doesn't seem like a soldier," Jace admitted, rolling over to watch Rory clean up Clary.

"It's cause you've never seen him when he's angry or bitter," said Amy, and her memories swirled around her, not all of them happy. "He's like a storm sometimes, horrible and furious, but he always comes back. He's always that happy boy in the end."

Jace considered the Doctor and decided that maybe there was more to the man than his happy smile and his bowtie and his time machine. "He'll have to be furious if he's going to fight Valentine."

* * *

Clary didn't know how long she had been asleep, but when she finally managed to shake herself free of the grip of the sedative, she found herself in a dark room, tucked under a number of blankets, beside Jace. Jace was, himself, asleep, and Clary was pleased to see that he was sleeping soundly; the recent months had taken their toll on him and Clary thought if anyone deserved a good, long sleep, it was Jace. She snuggled up closer to him and Jace stirred in his sleep.

"Don't wake up," she whispered softly, pressing his hair off his face. "Just keep sleeping."

Maybe his subconscious heard her, because a moment after Clary had spoken, Jace's face relaxed and his body melted to fit around hers. As she curled up against Jace, Clary tried to recall the steps that had brought her here. The memories came in reverse order, and they came slowly. She saw herself being tucked into bed by the kind-faced Amy Pond, and then Amy dressing her in pajamas. Before that, there was the hectic journey through countless halls, drenched in blue light, and there was the impossibly huge room, hidden behind the deceiving wooden doors of the police call box. The blue call box. It was the blue that triggered it all, that pleasant blue color that made the artist in her smile faintly.

_I'm in a huge box, _Clary thought, smiling crookedly. _I'm in a space ship, time machine hidden in a blue box, traveling with an alien and a nurse and a model. _The entire concept weighed down on Clary for a while, and she lay in bed, feeling her heart race. But, eventually, as she thought and thought about it, breaking it down as best she could, her mind wrapped itself around the idea. _I've met werewolves, vampires, warlocks, angels and demons, and those are just as alien as a man from another planet, right? The Doctor is just like Luke, he's a person, just not a person like me. And the Doctor can travel through space…well, so could Magnus with his portals, so that makes sense. He's just a person who can travel through space…and time._ It was that last part that still got Clary, but she tried not to dwell too much on it.

However, it was time that jogged her memory and made her stomach clench. "Time!" she cried, and sprang up. "Oh, god, how much time have we spent here? How long have we been here?" Her shouts had woken Jace as well as activated the lights in the room. She was pacing so frantically she didn't even notice that her feet didn't sting, that her cuts had been cleaned and bandaged, and her bones set. "Jace, my father's going to murder us!"

Jace had woken with a start when Clary had screamed, and he was watching her warily from the bed. He'd been having the best sleep he'd had in months, and for some reason, he didn't want to pull himself up from the blankets and get Clary; he wanted Clary to get back in bed with him. "Clary, I don't think we're going back to Valentine."

"Going back?" Clary laughed hysterically. "It's not about _us _going back, it's about _Valentine_ comingfor us. He's going to track us down, Jace, you know he will. He's never going to let us go, he thinks he owns us-"

"He hasn't come yet," Jace pointed out, feeling his body sinking into the bed welcoming. For some reason, he couldn't take the threat of Valentine seriously when he was tucked comfortably in bed, all his injuries set to healing. "Maybe he really can't reach us here. The Doctor did say we're in another dimension."

"_Jace_," Clary said, exasperated. "You know him better than I do, and you know he'll burn this world down just to get his hands on us. There's nothing this Doctor can do to stop him."

Jace bit his lip. "He-he's done _a lot_ of things, Clary," said Jace, thinking of the stories he'd heard from Rory and Amy. "He might be able to help us."

"No, that's impossible," said Clary firmly, and she started digging through the pile of, now laundered, folded clothes at the foot of the bed. How long had they been there? "Where's the phone? I'll call him, I-I'll try to calm him down, maybe he won't be too furious."

Jace thought of Clary calling Valentine, and wondered fearfully if Valentine would be able to track them through because they owned and used the phone. "No, Clary!" he cried, jumped up, just as the door opened and Amy and Rory tumbled in, in bed clothes, with sleep lines under their eyes.

Clary had untangled her phone from her jeans, but she dropped it almost at once. Her face was pale and she looked ill. Slowly, her eyes lifted up to Jace. "He-he called us, Jace. There's a message from Valentine on the phone."

Amy hurried over, scooping Clary up onto her feet and rubbing her back. "Don't worry, Clary, don't worry. Why don't you get back into bed and rest? You need it."

But Clary wouldn't budge. "I'm not going anywhere but back to my father."

"_Why_?" demanded Rory, who had plucked up the phone like it were rat he'd found in his home. "After everything he's done, why would you want to go back to him?"

"He's going to find us anyway, don't you understand? If I go back to him, maybe he won't be too furious. Maybe he'll be merciful," she said the last word softly, like a prayer. Jace's eyes were sympathetic, but he knew Valentine was never going to show them mercy. "You have to let me go," Clary begged. "I understand if Jace stays, I can go back alone. He might not come after you if I go."

"You're not going _anywhere_ without me," Jace growled. "And you're not going back, not if I can help it. Play the message," he added to Rory.

Rory flipped the phone open and stared at it curiously a moment; phones from 2007 were a great deal different from 2011. After a minute of fussing, Valentine's smooth voice was heard around the room: "Clarissa, Jace-it seems you two have finally decided to run off, and I must tell you, as your father, and your master, I am not pleased. I thought perhaps I might have taught you both enough to know that I don't brook disobedience. Now, I don't know where you've run to, or how you've evaded my Tracking rune, but I'm going to find you, and I am sorely amiss if you don't live to regret your escape attempt. You can return to me, or I can hunt you down and bring you back, but either way, I will not show you any mercy. I do not accept dissention among ranks."

His voice ended abruptly and Clary, still in the circle of Amy's arms, gave a cry of pain. He wasn't going to forgive them anything, even if she called him now and begged him. Clary started to shake and Amy sat her on the bed so Jace could take her in his welcoming arms. He kissed her hair even though he himself felt shivers racing up his spine. "It's going to be okay, Clary, I'll try and take care of things."

"No, you won't."

They turned, and there, in the doorway, leaning against the frame, was the Doctor. His head was bowed as if he were in deep contemplation. Jace thought he saw a flash of the man Amy and Rory spoke of, a flash of the soldier who had done the impossible, but it was darker still. There was something about him, some contained, immense power that hung around him like an aura, and Jace wondered if maybe Valentine had met his match.

"Give me the phone," ordered the Doctor, sweeping past them and tearing it from Rory's hand. "I'm calling Valentine."

"Wait-" Clary tried to protest, but the Doctor simply raised a hand and pushed buttons until the phone rang.

Valentine must have been waiting for the call, because when he answered, it was still smooth, but there was furious undertone. "Clarissa, I was wondering when you'd work the nerve to call. Tell me where you and Jace are, and we'll make this as easy as we can."

"This is isn't Clarissa," said the Doctor and his voice was like steel.

"Then who may I say is calling?" Valentine asked rather politely.

"We've met once, but you knew me as Mr. Smith then." The Doctor paused, trying to gather himself when he saw the look of raw terror in Clary's eyes and the veiled fear in Jace's. "My name is the Doctor, and I've taken your children away, and I wouldn't bother looking for them. You'll find it quite impossible."

"You'll find me, _Doctor_, a very capable man, especially when my things are called into question." Valentine's voice grew hard. "You have no understanding, young man, of who you're dealing with."

The Doctor laughed, but there was no human in his voice. "I was about to tell you the same thing, Valentine. You may be a shadowhunter, and a well-trained one at that, but I'm the Doctor."

"So you know what I am?" asked Valentine, amused. "Good for you, little Mundane."

"I'm _not _a Mundane," warned the Doctor, and Clary was impressed by the anger in his voice. "I am the Doctor, the Oncoming Storm, the Destroyer of Worlds, the Timelord Victorious, the Predator; I alone walked away from the last of the Great Time Wars, I have turned back time, walked in universes outside this one, I have fought angels and demons, I have held the fate of the universe in my hands more times than you've drawn breath. Do _not _try to intimidate me, Valentine Morgenstern."

When the Doctor stopped, Valentine was still silent, not sure whether he believed the man. He decided he didn't. "I will track down my children, Doctor."

"You'll be hard put to do it, Valentine. Jace and Clary are with me, on my Tardis. There is no army you could summon that could breech my ship, but, feel free to try. While we're on the subject, you might be interested to know the Tardis is space ship as well as a time machine. I am taking Clary and Jace well beyond your reach."

"I won't have my children stolen," Valentine said simply. "If you take them, you'll have me to face, and I don't think you quite understand the implications of that. I have the army of heaven and hell behind me."

The Doctor looked down then on Jace and Clary, and he saw them curled against each other, united in their fear and exhaustion of Valentine. He had spoken to Rory and he knew the extent of the damage done to both of them, and worse, for Valentine, at least, was that the Doctor blamed a great deal of their suffering on himself and his inability to act, to save them before Valentine had hurt them. Now, the Doctor was determined to set to right what he should have done a long while ago.

"Good, because you're going to need all that and more if you want to fight a Timelord, Valentine."


	9. Dust

**Hey everyone! Sorry this is so late, but I underestimated the amount of time I'd need to dedicate to research. I'm still trying get both stories updated once a week, but it might be difficult. I will say though, that I'm loving it here, and I guess the happiness just seeps in because I've decided the next chapter will go out in a proper Doctor Who adventure. It'll be fun!**

Dust

_The way I see it, life is a pile of good things and bad things. The good things don't always soften the bad things, but vice versa, the bad things don't necessarily spoil the good things, or make them unimportant_

_-The Doctor_

Jace and Clary looked at the Doctor, their mouths open and their eyes wide; in his life, Jace had never once seen or heard someone speak with his father like that. He could remember times that he might have made his opinions heard to Valentine, but he had never once dared to be so forthright or direct with him. A few of the names the Doctor had used chased each other across his mind: _Timelord Victorious, Destroyer of Worlds, Oncoming Storm…_They were vaguely terrifying, but Jace couldn't put an actual event to a name, so he didn't understand the full implications behind each one. He did know, however, that Clary was sitting beside him, looking practically horrified.

The Doctor tossed the phone to Clary and Jace on the bed, but when he looked at them, he was smiling like a boy again. It was as if all that he had just said had never happened and they were again in calculus lecture. "Well, that went well, wouldn't you say? Hardly a death threat at all. So, where do you feel like going to today? The Tardis is in much better shape now that I've picked you two up."

"Go?" Jace said. "We can't _go_ anywhere. Valentine is looking for us right now, and he's going to notice if a blue box goes soaring through the air over New York, don't you think? We need to lay low."

"Well, that's what I'm saying!" the Doctor exclaimed, ecstatic. "We need to get out of here for a little while, let him cool off and regroup. What do you want to see?"

"What do you mean, what do I want to see?" Clary asked, measuring the Doctor. "You mean, take us somewhere?"

"Of course," laughed the Doctor. "Somewhere to help you relax and breathe a little. You look practically petrified."

"You just verbally attacked the man who had been torturing me for the past six months. Yes," said Clary a little angrily, "I am petrified."

The Doctor looked shocked that Clary would be scared of anything; after all, she was on the Tardis now, but he knew a look of fear when he saw it. "Tell you what, I'm going to show you two something wonderful, something amazing, something that will make even you, Jace Lightwood, look twice."

"What?" asked Jace, unsure whether he was amused or annoyed with the man.

"Get on your dressing robes and meet me down stairs!" he cried, tipped them a bow, and fled.

Clary watched him go with suspicious eyes. "I don't think I can trust a man who seems to constantly to be either a child or a god."

"You'll get used to it," shrugged Amy, who was smiling a little more than she meant.

* * *

Jace and Clary stumbled down the grated steps of the Tardis, looking more than a little bedraggled with their robes a size too big on their painfully thin frames. Rory was quick to notice how malnourished the children were, and wanted to stop and get them food from somewhere. However, it had seemed that the Doctor had other plans, as he was circling the Tardis controls, flipping switches as he went. When he saw them approaching, the Doctor shot over to them, his face clean of any residual anger he might have felt for Valentine.

"So, you two, have you given any thought as to what you want to see?" He looked excited, just like the teacher he had been but a day ago. "There's a whole universe out there!"

Clary glanced over to Jace who still seemed unwilling to believe that the Doctor could time travel. "You said you could take us away," she finally said. "You said you could take us so far away from my father he'd never be able to track us. Even in his wildest dreams."

"I did say that," agreed the Doctor slowly and his face was glowing. He leapt suddenly into action, dashing back to the counsel and waving them all forward. He began speaking, his habit of talking too fast for anyone to really understand making an annoying return. "Yes, so, we'll go somewhere Valentine can't reach. I'll take you right out of this city, right out of this world. Maybe we'll make a quick stop over at the Horsehead nebula, maybe stop at New Earth for lunch, and then, then we'll _really_ go! Other side of the universe, that's where we'll go. Sound nice?" In response, the children's stomachs gave loud growls. "New Earth before the Horsehead nebula, then. Now, hold on tight, because I've got to show you something first."

"What?" asked Clary, watching both Amy and Rory taking a firm grip on the counsel, and then taking one herself.

Instead of answering, the Doctor slammed his hand down, hitting buttons and throwing switches. Very suddenly, a loud sound, like the pounding on a drum or the air being sucked up by a vacuum was heard. Jace gave a shout of surprise when the Tardis began to shake, and he felt his hands convulsively grab the railing for support. All around them, the room was trembling, the sounds of grinding and groaning echoing through the chamber like an angry car. They were being tossed here and there, just barely managing to hold on to and all the while, the Doctor was whooping with joy. Clary checked over with Amy and Rory, but the two wore the same expression: a tired kind of joy. They clearly loved it, even though it wore them out to travel.

However, the Tardis began to slow, and Clary could feel her feet beneath her again. She breathed a sigh of relief and look over to find Jace looking stricken. "What was that?" he asked in a hoarse voice.

"We're here!" the Doctor announced jovially, running his hands through his hair. "Perfect landing too."

"What's here?" Jace asked for both he and Clary.

"What I want to show you before I take you anywhere," answered the Doctor in a quieter voice. "It's very important that you see what I've got here." He jumped away and stood before the wooden doors, his face a boyish grin. "Come see what I keep in here."

Jace helped Clary down unsteadily and the two joined the Doctor before the doors. Partly, they thought he had brought them back to New York and were wondering if Valentine's threat was too great. Secretly, Clary hoped the Doctor was being true to his word and showing them something wonderful.

"What do you keep there?"

The Doctor threw open the doors and stepped aside. "Everything."

Clary gasped and Jace felt his mouth hang a little loose. Behind the Doctor's doors was nothing, nothing but the black void of space. However, here and there in the black was the faint shimmer of stars, and, as they inched closer to the door, they saw what the Doctor had meant them to see. A huge nebula hung across from them, almost as if painted across the skies. It was purple and pink and red, bursting with the light so bright it blinded them at its center. Jace drew close enough to look out completely, and his stomach rolled when he saw beneath him the nothingness of space. His mind raced to understand what it would be like to step away from the wooden floor and simply float forever in the antigravity of the void. Clary, beside him, trembled, and Jace knew it wasn't from fear.

"What is this?" she asked in a whisper.

The Doctor leaned against the door frame, surveying the beautiful image before him like it was a rare and valuable painting. "It's the Earth-Earth after the sun's dies and it finally falls apart. We're hundreds of millions of years in the future. Hundreds of millions of years away from Valentine."

Clary hung back, but she wanted to reach out and touch it. "It's beautiful."

"Yes, it is," he agreed. "It's the power of time; it alone has the ability to crumble everything to dust-including Valentine. And me," here, the Doctor smiled faintly, "I'm a lieutenant of Time, the man who does her work. So, no matter how powerful he may seem, your father, he's nothing but dust compared to me."

Jace gawked at the dust spreading slowly out before him. "Can you show us more?" he finally asked.

"Jace, I'll show you everything if you want me to," replied the Doctor in his kindest voice. "Everything you've ever known to be real, I'll show you better. I'll make the life you've known nothing but a distant, dull memory."

"But can we stay here a bit longer?" Clary asked quickly. "I-I like to watch the dust float."

"We'll stay as long as you like, Clary," assured the Doctor. "How about you two sit down before you fall over? I'll see if I can't find a kitchen somewhere on this ship, and me and Amy and Rory will fix you something to eat."

"It takes all three of you?" asked Jace, though the sarcasm was veiled by the wonder of the dead earth.

"Yes, unless you like fish sticks and custard."

Clary and Jace both sank down onto the floor of the Tardis and dangled their feet over the edge into space. The ship slowly circled the cloud that had been Earth, as though it wanted them to see all the possible views, all the destruction, all the beauty. Clary felt the erratic beat of her blood in her veins die down, and her mind relaxed. She was at peace again, a feeling that had been missing from her life since before she'd even met Jace. All her fears melted away, all her worries and pains floated out to join the dead earth. At her side, Jace was enthralled by what he was seeing. All his life he had known only the power of a warrior tested against the power of demon, but what was that power compared to the pure destructive force of time? In the end, it all fell apart, so who was he to fight it?

"Do you think he can help us?" Clary finally asked, her eyes reflecting the earth.

"I think he's the only one who can," Jace said after a beat. "I think he is who he says he is, and I think who he is, is a very powerful man."

"He was a bit scary back there," admitted Clary. "When he was talking to Valentine, I mean. Have you ever met anyone who speaks to your father like that?"

Jace gave a hollow laugh. "No, no one speaks to Valentine that way."

"But, he was scary. Terrifying, even," whispered Clary.

Though Jace didn't like to admit he was afraid of anything, he couldn't deny that there was something about the Doctor that made the hair on the nape of his neck stand on end. "Yes, I think he can be when he wants to be. Amy and Rory told me he fought in a war once, that he was soldier, and I think that left a mark on him. I think he had a good heart, but there is a part of him as dark and cold and cruel as Valentine. Maybe even more."

"He's seen so much," mused Clary. "He must have lost so many people, so many friends."

"That will make you hard," Jace said thoughtfully and then stirred from his dark thoughts. "I wonder if he'll be able to find the Lightwoods, he had Isabelle's bracelet, after all."

Clary nodded to herself. "I think he'll help you if you let him. I think there isn't anywhere he can't take us, or anyone he can't take us to. At least, he seems to make it seem that way," she added as an afterthought.

They sat watching the dust of earth float away into the void until Amy arrived and tapped them both on the back. She was smiling down of them with crinkled eyes. "So, Rory is about to throw a fit if you two don't get some food in you, going on about your health, so, do you want to come to the kitchen and get some food? We've made some ham and potatoes and veggies, and, honestly, you two look a bit peeked." Amy eyes raced down Jace and Clary; their clothing did seem to be hanging off them.

"Ham?" asked Clary, and she felt her mouth water and her eyes slipped over to Jace. "It can't hurt to sample what our hosts made."

Jace laughed. "Well, lead the way, Amy."

Amy ushered Clary and Jace away from the open doors of the Tardis, though they both felt the wonder almost as a physical thing. Again, it seemed the Tardis was made of infinitely many passages that were lit from the glowing blue heart that was the Tardis. When they finally found the kitchen, Clary felt her hand clutch on Jace's. Rory and the Doctor were seated around high table, plates before them, forks in hand. The smell of freshly prepared ham was wafting through the air, and Clary inched in closer

"Found the little ones." Amy pressed on their backs, directing them into the kitchen. "Staring at the earth like they'd never seen it before. Rory, stop being lazy and make them a plate." She shooed them to the table where the Doctor was watching them contemplatively.

"Did you like what you saw?" he asked, giving them his usual boyish smile.

"It was incredible," Clary answered, and her voice was weak, but not from its usual terror. "I don't understand how it can be-well, how the Earth can be there when we were just there. We must be millions of years away from where we were. But we can be back in less than a minute."

"Yes, time travel does that to you," the Doctor said, not the least bit confused by what Clary had just said. "You'll get used to it if you stick around a bit longer."

Jace gave the Doctor a considering look. _What had he meant by stick around a bit longer? How long can Clary and I stay here? What about our friends and families. _"Speaking of the Earth, though, I had a question about the Lightwoods."

"Yes, Alec, Isabelle and Max," said Rory and he produced two plates full of food. "They were very worried for you"

"I've was curious; have you spoken to them about escaping?" Jace asked. Though he tried his best to sound nonchalant, there was a fear for his family that he couldn't disguise. "Or, would it be impossible at this point?"

"No, not at all," said the Doctor. "The necklace Isabelle wears is quite unique and gives off a special kind of radiation the Tardis can track. We'll get right on that."

Jace swallowed back a loud expletive. "We're going to help them…just not now?"

Clary, like Jace, didn't raise her voice-she barely raised her head from the plate-but she said, "Once my father finds out that we have really gone, he's probably going to go after Jace's family. He'll use them to draw us into a trap, and, quite possibly, hurt them once he finds out the role they played in our escape."

"How could he know?" asked Amy, sensing Clary's discomfort.

"What's left of the Silent Brothers now serve my father," Clary explained. "He's been using them to hunt down any pockets of resistance that still fight him. He'll force Alec and Isabelle at least, maybe he'll spare Max."

"Well, that's where the time travel part comes in." The Doctor began gesturing wildly with his hands. "Even if you think in the sense that all the time we're wasting right now is time for Valentine to bring the Lightwoods to him and hurt them, that's only _one_ reality. Once we return to a time almost directly after I took you two out of the school, the reality that they were in ceases to exist, and the new one takes its place. It's called an aborted time line."

"Something like that happened to me," Amy said quickly, seeing the blank looks on their faces. "The Doctor was supposed to be killed by River, but she didn't do. Instead of the time paradox resolving itself, though, it started an entire new universe. In that universe, I killed a woman, but when I got back, it had never happened. An aborted timeline."

"So everything that's going on right now there, isn't going to be happen?" Clary clarified.

"Right," said Rory. "It will be like a bad dream."

"But," Jace cut in. "If you still remember what happened to that woman, even though technically, it didn't, won't Isabelle, Alec, and Max remember what happens to them?"

"No," the Doctor shook his head and waved around them at the inside of the Tardis. "You two have taken yourselves out of the time stream just like Amy and Rory did. Once you're out, the laws of time and space change for you. For instance, there was time, a long time before Amy and Rory traveled with me, that a man named the Master enslaved the world. I did a thing, and stopped him and turn time back, but the only ones who remember it ever happened are the people who were with me. Amy and Rory don't remember it, but the woman who was my companion does."

"You did a thing?" Jace raised an eyebrow.

"Yes, a thing, respect the thing," said the Doctor distractedly. "The point is, the laws of time don't work the same for you anymore because you've stepped outside the time stream itself. Think of it like stepping outside a grid: everyone else is in it, but you're gone."

"They won't remember though?" pressed Jace.

"No, no they won't remember a thing," he said easily and then his eyes narrowed in frustration. "That's not the real problem. What we really have to figure out is what caused this time stream in the first place. This _literally _wasn't supposed to happen. You two were supposed to stop Valentine at the beach on Lake Lyn. Something went wrong, or something might have gone right, and it resulted in Valentine winning."

"And we need to know what that is?" Clary asked.

"Well, I want to resolve the paradox while I'm here," he said reasonably. "Normally, with time abnormalities, the paradoxes resolve themselves-it's what makes time travel possible-but if the paradox isn't resolved, we could end up with a tear in the universe the size of the Milky Way."

"This might sound silly, but what's a paradox?" asked Clary, seeing Jace's confused face as well.

"Let's say you go back in time and kill your father before you were born. If you're father dies before you're born, then you can never be born in the first place. If you're never born, you can't kill your father, thus, the universe stays the same." The Doctor said all of this fast. "That is one way the universe usually resolves paradoxes, unless something a bit odd interferes."

"Won't it fix it on its own then?" Clary asked.

"Well, that's the odd bit I mentioned," the Doctor said, and he looked slightly nervous. "See, most paradoxes can fix themselves, but sometimes, it's very hard. For instance, let's just say I was supposed to die and I somehow managed to avoid death. This is a problem for the universe because I'm immortal. For most people, if they were supposed to die and didn't, well, they would die of normal causes in, at most, a hundred years. That's a very small tick in the time of the universe. For people like me, though, a usual timescale won't kill me.

"If the problem with the time line here is something like me, then it won't work itself out and it could be very bad. See, there have been times I was supposed to die, and I didn't, and it was bad. In fact, when I _didn't _die, time almost died in my place." The Doctor shrugged off their stares. "I want to make sure that whatever caused this, isn't like me."

"Sounds like is should be easy," Jace said cautiously. "Something happened during that last week that really messed this up."

"It should be simple, but I just _can't _figure out what!" the Doctor cried, and gave himself a furious shake. "I mean, it has to be staring me in the face, but I just can't see it. I'm blind to these obscure small detail sort of things."

"You think a person's like is a small detail," said Jace, but his eyes were smiling a little.

"Well," said the Doctor, fussing with his suspenders this time, having tired of his bowtie. "I mean to say, there's a lot of people in the universe, you wouldn't believe how many, and when I'm the one saving _all of them_ a single ape-descent earth life form doesn't exactly take the cake."

Jace tipped his head and returned to his ham. He hadn't had a proper meal in too long to remember, even the food Valentine had allowed him had felt like ash in his mouth anyway. This had a much better flavor to it. Or at least he didn't feel like a dog getting a treat for being good while he ate. When he glanced over to check on Clary, he found she had already finished her plate and was eyeing the potatoes still steaming on the counter. Amy smacked a pile on her plate.

"I heard you were married," Clary said conversationally, feeling uncomfortable with the Doctor's thoughtful stare resting on her face.

The Doctor flushed, charmingly, like a little boy, and smoothed his hair back. "Yes, River, she's quite a…woman." His pause only made Clary giggle.

"She must be if she's alright with the whole time travel thing," Jace commented, again, looking about the huge interior. "I take it she's the same, um, _type of person_ as you?"

"No, nothing like that. She's got her own gun!" The Doctor laughed as if it were the most ridiculous notion, but then hurriedly changed the subject away from it course: his own past, his own dark crimes. "So, how do you feel about a trip with me? Just one for fun, a little spin across the universe, see some sights, maybe meet a few new races. I can have you back by five minutes ago if you like."

"It seems like we shouldn't," Clary hedged.

Rory, who knew that Clary and Jace, though he'd never admit it, were both in a delicate stage of recovery, the psychological process. The healing of the mind is always a hard thing, and for two children in a situation they were in, no small matter. He figured the more time they spent away from their current situation the better.

"You'd like it," Rory said loudly. "Really, the Doctor knows this universe inside and out. I mean, seeing the earth was amazing right? What about another planet? What about like on Mars?"

"What about a galaxy on the other side if the universe?" Amy piped up.

Clary looked nauseous. "Do we have to go so far?"

"Not all!" the Doctor crowed, jumping to his feet. "We can stay right here in this galaxy if you want. I can take you to Earth, but one you've never known: older or newer. Or the moon once it's colonized. Or Mars-Mars is great in the summer, they do wind surfing in the eye of the red spot!"

Clary knew that she was going to say yes, but her heart was unsettled by it. It didn't seem right, running off; at least, it didn't seem right _then_. "Just a quick trip. Something more at home?"

"Clary likes to paint," Amy said suddenly. "You know a painter or two?"

"Van Gough?"

"And Jace likes to play the piano," Rory put in.

"Beethoven? He owes me a concert anyway," shrugged the Doctor. "I practically _wrote_ Fur Elise."

Jace smirked, but when he saw that Amy and Rory accepted this with nothing more than a blink of their eyes, he gave a double take. At his side, Clary giggled again. "So surprised Jace?" she asked as Amy went around, collecting plates.

"I don't get him," Jace said, frustrated. "I don't understand how he can be so damn nice, so innocent to the world, and then, turn his cheek, and be some great warrior from another time. I've spent my entire life fighting a war, Clary, and those two things can't go hand in hand."

"I think you've never met a person like him because there is no one else like him. I think he's proof that just because you can fight, doesn't mean you live by it." Clary seemed pleased with her wisdom and jumped up when Amy touched her on the shoulder. "Are we going somewhere?"

"I think we're making one stop before we head off." Amy's eyes twinkled. "You'll love it."

Clary and Jace followed Amy, this time much more willingly, to the control room of the Tardis. The Doctor was already flipping switches, throwing levers, twisting knobs when they arrived, and as soon as he saw them safely inside the main room, he threw the stops and the Tardis lurched into motion. This time, though it was still the same stomach churning sensation, Clary found it oddly exciting, like a roller coaster: it was terrifying, but in a good way. As the Tardis slowed to her usual relaxed pace, Clary's eyes moved expectantly to the door.

The Doctor caught her looking. "Scared?" he asked, his eyes glimmering.

Clary took Jace hand in her grip. "What you got?"

"I love it!" cried the Doctor and he raced to the door. He threw them back, calling out, "Would you look at this!"

Amy gave a delighted screech and Clary gasped, Jace, at her side, smiled down, but it was Rory who seemed to have a voice. "What am I looking at?" he asked, not unkindly.

"Stardust," answered the Doctor grandly. "Some of the most valuable, amazing stuff you'll ever find the universe, and I'm going to tell you why." He waved them forward and the small group of humans joined him at the door.

Before them hung a cloud of white and blue dust, sparkling like small diamonds in the sky. The cloud looked like all the pictures Clary had seen of nebulas in pictures from NASA, and she had a terrible urge for a pencil and paper to draw. With a start, she realized it had been months since she'd drawn anything that wasn't a rune for her father. Still, looking at their circles of dust, her heart stirred.

"Your bodies," began to the Doctor, sounding like he'd swallowed a text book. "Are made of elements, all of those elements are found combusting in the heart of stars. In fact, when this universe was in its infancy, that's all you had was huge, bursting stars, spreading their insides all across the universe. Those elements came together again and made the planets, the new stars, and you." His voice was suddenly far away, a distant smile touching his lips. "We're all children of stars."

"That's beautiful," Clary said kindly.

"That's the truth, which, of course, is a beautiful thing." The Doctor nodded sagely, then, like the half crazed man he was becoming, pulled out two mason jars. "The reason I've brought you here is for this. A nice souvenir, yes, some stardust?"

Jace gaped. "How do we get it?"

"What do you mean? You just reach the jar out and scoop some up. We're in space, it's not like it's going somewhere fast. Here, take the jar," the Doctor thrust the jar into Jace's hand and ushered him to the threshold of the Tardis. "Now just reach your hand out and scoop a bit in, like water."

"There's no oxygen."

"I've extended the oxygen field around the Tardis, don't worry, you'll be fine. Go on!" he urged, and Jace carefully stretched his arm out.

At first, he felt only cold, and he suspected that was space, but his arm wasn't freezing off and he could feel his lungs fill with air, so he risked a balance on one foot to better get at the dust. After a moment of floating nearer and nearer, small bits of something began to pelt the inside of the jar. Jace jerked his arm back in and found the jar full of something white and grey and black, slightly iridescent, and beautiful.

"Max would have loved this," he said breathlessly.

The Doctor, who had been enjoying Jace's amazement, jumped like he'd been stung. "What did you just say?

"Max," said Jace faintly, still smiling at the glowing particles in his hands. "My little brother, he'd love this. When all of this is over, Doctor, will you bring him here and show him this. I think he'd really love it."

Amy and Rory knew the Doctor too well not to miss the look of terror on his white face. When he saw them looking, the Doctor quickly composed himself, but they had seen the dark, worried look in his eyes. "Yes," the Doctor replied slowly. "Yes, I'll bring Max."

The Doctor shuddered. The paradox was revealed: Max Lightwood was still alive.


	10. River

River

_You might want to find something to hang on to._

_-River Song_

One thumping, bumping, lurching, groaning time ride later, Clary and Jace found themselves waiting apprehensively as the Doctor fiddled with the controls of the Tardis, checking that it was properly locked in place, as it had been known to "wander off to the Middle Ages" on more than one occasion. He gave it a good whack before turning to face them, and then smiled broadly, like the boy he always appeared to be. Clary felt her heart beat a little faster as her eyes trained on the door. What was waiting out there for them?

"So, you two shadowhunters think you've seen it all? Think the world doesn't have any more secrets?" he was joking with them, they could tell; he had long since revealed the kindly man behind the soldier. "Or, do you think you're ready for one more adventure?"

Clary grinned like a little girl. "It'll never hurt to find out."

"_Love_ the spirit." The Doctor clapped his hands together, contemplatively. "So, there are a few rules I need to go through with you two. One, try not to make history before it happens. I know everyone wants to be famous and all, but it really messes with the flow of time, unless of course, you were supposed to do it. In that case, do it." Clary and Jace smiled at each other. "Next, if I say go back to the Tardis, get back in the Tardis. I don't know what's out there, but if it's dangerous, I don't want you two getting hurt. _And three_," and here he paused, and his face was very serious and Clary thought that maybe his games were over. He drew closer to them so he could lower his voice. "If you see a fez, pick it up."

"A fez?" Jace couldn't keep the disgust from his voice.

"Fezzes are cool," confirmed the Doctor, mistaking, or ignoring, Jace's disgust for amazement. He then dashed past them and threw open the doors to the Tardis.

Bright sunlight and the strong smell of sunflowers met Clary and Jace as they emerged from the Tardis interior. Clary covered her eyes, trying to peer into the blinding light, and her hand reached out and snatched up Jace's. At her side, Jace was just able to make out a dirt road bordered on all sides by towering sunflowers.

"Where are we?"

"Provence, France, in the year 1885. Tell me, Clary, since you're a little artist, which famous impressionist lived in Provence, France in 1885?" The Doctor was glowing with excitement.

"You can't mean Van Gogh?" Clary peered about as if she expected him to emerge from the flowers.

"The very same. We've been here once before, so I guess a little check in on Vincent can't hurt. He seemed to fancy Amy. Why don't we see just how he's been since we were here?" The Doctor took off at a jolly pace, Amy and Rory behind, while Clary fell into line next to Jace, her mouth agape.

"Van Gogh? He's not serious, he can't be. He was one of the greatest painters of all time." Clary still seemed highly suspicious. "Maybe I've gone mad."

"Then me with you because I'm seeing the flowers as much as you." Jace laughed and hurried her along.

They carried along the dirt lane awhile, enjoying the sunlight, when they crested a small hill and looked upon a quaint house. On the porch was a small table with chairs assembled around it, a vase full of blooming flowers in the center. The door was propped open, and from inside, could be heard singing. Clary felt her heart jump at the voice and she was taken by an urge to run down the hill side.

"Vincent!" cried the Doctor as they descended the hill. "Vincent, come out! It's me, the Doctor!"

The singing stopped abruptly just as they reached the stairs of the house. They heard a chair being shoved against wood haphazardly and then frantic footsteps. Clary craned to get a better look, and even Jace, though uninterested in most Mundane art, peered a little closer. The door almost flew off its hinges as a small man with red hair came bursting out, his face split in a grin. Clary had only a moment to take in his shirt, covered in a tattered, paint splattered over shirt, and loose pants, before he rushed down the stairs and threw himself at the Doctor.

"You've come back, Doctor!" he cried, sweeping the Doctor up into a hug. "A visit no doubt, to tell me all about the wonders of the universe? And you've brought Amy," he said, turning to her next and hugging her as well. His eyes found Rory, who seemed uncertain and a little awkward. "And who's this?"

"This is my husband, Rory," Amy said, pulling Rory forward.

"Married?" Vincent said, his face a mixture of sadness and intense joy. "Why that's wonderful, Amy." He shook Rory's hand and faced Jace and Clary. "Much time must have passed if you've gotten married, had your children, and watched them grow."

"Children?" Jace blanched.

"Oh, no, Vincent," said Amy quickly. "They're not our children, just some friends we picked up and thought we'd show them around. This is Jace Lightwood and Clary Morgenstern."

"Jace and Clary," said Vincent, and came forward, taking Jace into a one-armed hugged, and kissing Clary on either cheek. Clary, for her part, was too stunned to move, and stared up at him with wide eyes. "Friends of the Doctor's are welcome here always. Come in, come in and see what I've been working on lately."

He ushered them into his small home, Clary practically dragging Jace in her excitement to see. The inside was as simple as the outside, but for the color bursting off all the walls. It was sparsely furnished, though the chairs and tables it did have were well worn. It was, however, the art work that made its home within the walls that drew Clary onward.

There were paintings everywhere. Scenes of the country side, of rivers, of flowers, of grassy slopes; but there was more: street lined with shops, a girl and her dog, butterflies, deer, a winter landscape. So much color, so much emotion; Clary had dreamed of a place like this. She and her mother had used to toy with the idea of living as starving artists, selling their work and living in a small house, just the two of them. They would spend most of the day painting, drawing, sketching.

But the reminder of her dream brought back her mother, and she turned from it quickly.

"This place is beautiful," Clary announced, cutting Vincent off mid-sentence as he explained a painting he had just sold to an elderly gentlemen for his wife's birthday. "Your house is beautiful."

Vincent smiled. "Why thank you, but you don't need to flatter me. I know it's just some walls and floors."

"A true artist needs only that," Clary agreed.

"You paint?" Vincent asked at once. "I caught you admiring a few things."

Clary blushed. "I _wish_ I could paint like this. I've tried to learn all my life the things you do so naturally, but I just can't. I remember looking at books of your work in school. And, on the weekends, my mother and I would go to the art museum and we'd spend hours looking over your work." Clary stopped suddenly, looking down. "I suppose you don't want to hear me going on and on, though, you want to talk to the Doctor."

"By all means, Clary, come and join us." The Doctor waved her over. "She's the reason I wanted to swing by, Vincent. Clary is an avid artist, she's just a bit out of practice. I thought perhaps talking to you might help her out of her rut."

Vincent looked honored. "I would love to help a fellow artist. And you, Jace? What about you?"

Jace, for once, was silent about his passion for war. Clary got the sense that here, in the presence of both the Doctor and a gifted artist, he felt awkward in his skills. Maybe he felt fighting and killing was not so excellent after all. "I'm not really talented that way."

Vincent, for all his kindness, sensed a soul in pain. "We are all talented in our own ways, and all poor in other ways. Maybe you should try your hand at it? Clary seems happy with it."

Jace looked fondly over at Clary, who was already peering closely at a depiction of a beautiful butterfly perched on a flower. "I do not think my hands are the hands of an artist."

Vincent frowned, but then his eyes smiled. "You may not have the hands of an artist, but every man has the hands for a glass of wine. Would you care for a cup?"

"That sounds excellent," Jace said and went to join Clary. She was running her fingers gingerly over the image. "You really like this?"

"Jace," she breathed in awe. "I've spent my life dreaming of being an artist, I've admired men like Vincent since I could walk. To come here, to meet him, to maybe even talk to him, is like a dream come true. And after everything we've been through…Can it stay like this?"

Jace was surprised. "You want to keep traveling with the Doctor?"

"Not quite, I just want to be this happy, this amazed," Clary explained. "Can we live like this once everything is over? Once Valentine is gone and the world back to normal, will you come with me, even if I wanted to live like this?"

"Of course," Jace said at once, not even thinking. He had long since accepted that wherever he went, it would be with Clary. He wasn't going to lose her now. "If you want to live in a little wooden shack in a field of flowers, I'll follow you there."

Clary took his hand in hers. "With the Lightwoods too."

"Wine!" Vincent proclaimed, breaking up the conversation they were having. Jace was pleased to have something taking his mind off his lost siblings. "Here, here, Jace, have a sip. Good wine, French wine! Where did you say you two were from? Or should I ask when, seeing as you're here with the Doctor?"

Jace took the wine and sipped it. It was certainly much stronger than he was used to. "I'm from New York, in the United States, and we're from the year 2005. Clary and I are, well, we're living together and the Doctor found us."

Vincent smiled sweetly. "True love, there is nothing so fine, but for the woman herself." He winked at Clary. "Tell me, Clary, would you like to paint with me after our little talk? I was going to go up the hill a bit and see if I couldn't landscape the town below."

"I'd be honored," Clary whispered. "I haven't got the paints though."

"You'll barrow mine," he assured, and then went to join the Doctor. "Doctor, where did you find these two?

The Doctor had his own wine, which he tasted and then spat back out. "I always hate wine," he muttered to himself, and then returned his attention to Vincent. "Well, they were in a bit of a way, and my Tardis brought me to them. I couldn't leave till I fixed them up."

"What was the matter?" he asked, dropping his voice and watching the young couple go from piece to piece.

The Doctor's face fell and his eyes darkened. "It's a bit of a mess still, in fact, we're going back soon. I just thought they could use a break from it all. Clary's father has proven to be quite a problem, and until I sort him out, I can't go anywhere."

"And Jace?" he asked, eyeing the boy with the fair hair and deep, sad eyes. "I've never seen a face so drawn and fragile before."

"Fragile?" asked the Doctor. "You think he's weak?"

"No, just fragile," Vincent shook his head. "He seems constantly on the verge of falling apart, because of his love for Clary, or something else, I can't tell. He just seems tired and ready to quit. Are you helping them, Doctor?"

"I'm doing all I can for them," said the Doctor, but his mind was on Max, on the boy who should be dead. "It's going to be a little difficult to balance the whole thing out. For now, I'm just trying to take their minds off things."

Vincent shook his head, but his eyes were glowing. "So you brought them here? I'm honored, Doctor, but I don't know if I'm going to be all that much help."

"Clary seems happy enough to meet you," the Doctor motioned for her to come over. "So, to paint, or not to paint?"

Clary had already tucked a paintbrush behind her ear, and she looked quickly over at Vincent, trying to judge his reaction. "I'd like to, if you're still interested in sketching the hillside."

"Yes, yes, of course!" Vincent clapped his hands together and raced to get his things.

Clary glanced back to the Doctor, and she felt a sudden bust of emotion for him. "Thank you for bringing me here. I could never, in my wildest dreams, have come here."

The Doctor rocked back and forth on his heels, looking embarrassed. "Yeah, well, I thought it might be good for you to have some fun. Now trot along, Clary."

Clary didn't need telling twice, and a minute later, she was stomping up a hill beside Vincent Van Gogh, carrying two easels and a can of paint brushes. She couldn't seem to find words to speak with, and would just stare up at him, her eyes wide and her mouth always slightly agape. He would speak with her, tell her things about his recent works or the people who were interested in them, even tell her about himself and his love of the country. Clary could only watch him in wonder, never speaking.

When they reached the crest of the hill, Clary found herself looking down on a quaint city, tucked perfectly into the valley. She could see specks of people and red-roofed houses, a river that snaked through the city, and a small market area of wood and cloth carts. "I love sitting up here and watching the city."

Clary blinked as she set up her easel and tried to find her voice. "It's beautiful."

"Well, it's more than that," Vincent said, pulling out a paintbrush and dipping it in his usual blue. "It's just so much going on, so many lives, so many people, so many thoughts, and to just drown them all out and see it all. It makes me happy and sad at the same time."

"Sad?" Clary asked, wishing she could think of more interesting things to say.

"Sad because I'll never really be one of those people, but happy because I'll never be one of those people. Do you understand? Vincent gave her a penetrating look.

"You're an artist," Clary reasoned. "You have to see the world from the outside looking in, that way you can paint it. If you were one of them, you could only paint what's out. It's a curse and a blessing, I guess."

"And have you always seen the world that way?" he asked, sitting himself down on a low wall and beginning his strokes over the canvas.

"I used to," Clary admitted, feeling slightly sick. "Back when I lived with my mom, I always felt like I was on the outside. But, then I met Jace and the other shadowhunters, and I learned about my father. I was on the inside then. And I hate it."

Vincent glanced over at her and saw her face was sharp with grief. "You shouldn't hate how you live."

"I wish I could just go back." Clary didn't know why words were pouring out of her to this man she knew so well but didn't know at all, but they were, and she couldn't stop them. "Everything is so horrible now. I thought, once I was where I belonged-on the inside-life would get better, but it just got worse. Don't get me wrong, I have Jace, and I wouldn't trade him for the world. But everything else is just miserable and painful and I'm afraid I can't go back to how I used to be." Clary clapped a hand over her mouth, surprised by how much she had said.

It seemed, though, that Vincent was not shocked at what she has said. Instead, he placed his paint brush down and leaned back on his seat on the wall thoughtfully. "The worst thing in life is not to get your desire, the other is to get it, so they say. But tell me, Clary, do you think if none of this had ever happened, if you'd never met these shadowhunters, do you think you would be happier?"

Clary paused and stared at her canvas, wondering: she certainly wished she had never met her father or her brother, but this life had brought her to Jace, and she wasn't willing to let him go. "I guess I am happier."

"Another way to think of it," Vincent said. "Do you think the people you have met would be happier without you?"

This time, Clary knew the answer; it was almost as if her earlier conversation with Jace was resounding in her ear. "No, no they like me."

"Then just hold strong to that," Vincent said bracingly. "I'll tell you something Clary: I despised myself. Not long ago, I couldn't care less if I lived or died, for I had nothing and no one. Even now, in my loneliness, I could very easily sink back into my darkness, but then I met the Doctor." Vincent's eyes grew bright. "He showed me who I really was, he showed me how the world saw me. That's what you need Clary, you need to see how the world views you. Hold on to that."

Clary measured Vincent and felt tears pricking at her eyes. "It's been so-so _hard_ these past few months. I can't explain, but, I just wanted to die, and it seemed like everyone else wanted me to too." Clary heard a sob escape her and Vincent drew closer, his hand resting on her shoulder. "I had _nothing_, just my father, and he wanted me dead, and my brother, and he hated me, and my mother, and she ignored me. All my friends were gone, they might even be dead, and all the while, I just kept thinking, what did I do wrong? Why do so many people want me to hurt?"

Clary's voice was drowned out by her sobs and Vincent took her in a warm embrace. Her small body shook in his arms. "Oh, Clary, don't cry, crying never gets us anywhere. You said you had something?"

"Jace," Clary whispered miserably. "But I'm more a burden to him. I got him in so much trouble."

"I don't think you're the cause for his sadness," Vincent said. "I think he's quite in love with you, and he's in pain only when you are. If you want him happier, you might just try a smile yourself."

Clary shuddered and drew a deep breath, gathering up her remaining strength. "Sometimes, I think I just forget how. It's been so long since I've done something I liked."

"Painting is something you like," Vincent pointed out, nudging her in the direction of the easel. "Come along, Clary, pick up your brush and paint for Jace. Show him how happy you are."

Clary's shaking hands curled around the paintbrush handle and she began the now unfamiliar strokes of an artist. As she worked Vincent split his time dabbing his own paint and helping Clary with her own. The evening set in and Clary drew back from the canvas, and before her was a small but accurate depiction of the city below. It had been so long since Clary had last painted that she forgot the rush of excitement that followed a completed piece. She gave a gasp.

"What do you think, Vincent?" she asked softly.

"It's lovely," he said, and glanced over at his own half-completed image. "Let's take this back to the Doctor and the Ponds and Jace, and have a proper dinner. I insist."

When they returned, they found the Ponds seated at the table outside on the porch, cups of wine in hand, deep in conversation. They waved merrily when they spotted Clary and Vincent coming their way, and called out. In the distance, Clary heard the whoop of the Doctor.

"Where are Jace and Doctor?" Clary asked, ready to thrust the painting into his hand. "They're still here, aren't they?"

Amy rolled her eyes. "The Doctor can't stay in one place for more than five minutes. He and Jace took off almost as soon as you left, muttering something about Beethoven. How was the painting?"

"Wonderful," Clary breathed. "What do you think?"

Amy plucked it and spread it out on the table before her and Rory. "It's beautiful. You really are a gifted an artist. Just wait until Jace sees this."

"Are they coming back soon?" Clary asked, feeling a pang of longing associated with Jace.

Amy and Rory shrugged. "God only knows what they'll get up to."

* * *

"This is your fault," Jace hissed, pressing himself as flat as he could be against the brick wall, eyeing the Doctor with as much dislike as he could.

"This is entirely _not _my fault," the Doctor denied, fiddling with his bowtie. "How was I supposed to know the man was a duke?"

"I don't know?" Jace shot back, lowering his voice to a whisper as he heard the sound of distant horse hooves. "Maybe when he was introduced as _Archduke Rudolph, patron of the arts_? But no, you were too busy messing with the half-finished sonnet, going on about strings and keys, to pay attention."

"First off, it wasn't a sonnet, it was symphony; and second, what type of man expects you to kiss his ring when you meet him? I was under the impression that you kiss cheeks when you meet!"

"I was under the impression you weren't an absent minded, time-traveling, lunatic, but I suppose I was wrong, wasn't I?" Jace heard the horses draw nearer. "If they find us, we can say goodbye to our heads."

"Did he really call for the police?" the Doctor asked, unable to help himself.

"Yes, he really called for the police." Jace rolled his eyes and peeked around the edge of the building they were currently hiding behind. "And they're coming our way now, so, do you have any more bright ideas to get us out of this one, or should I just have Clary find me a nice casket? A little short maybe, don't want her getting ahead of herself."

"Oh, ha ha," laughed the Doctor. "You really are overreacting. All we need is a little distraction for the time. Something to keep the soldiers off us while we make a run for it. The Tardis is just around the bend."

"A lot of good it does us there," Jace grumbled, and then snapped back around. They were at the end of line, trapped in an alley way, about to be arrested and executed by German police all because the Doctor had poor etiquette skills. Jace watched him fumble around with the screwdriver, whacking it against his hand and sighed. "Is this the sort of thing that happens often around you?"

"No," said the Doctor, and then a cry went up in German, and the men came rushing down the line. The Doctor blinked and then smiled uncertainly. "Well, yes."

"We're dead," Jace said faintly as a group of four men rounded the corner and came upon them.

"Hello!" cried the Doctor, sweeping his arms around. "What can we do you for today?"

"You are the Doctor," said the lead man. "And you, boy, are his companion."

Jace flushed. "I am not!" he snarled.

"Silence. You two are under arrest and sentenced to death by beheading-"

"Well that's a bit extreme, don't you think?" the Doctor said loudly. "I mean, all because I kissed a man."

"Poor choice of words," Jace muttered as the soldiers stammered their angry replies.

"Ah, yes, sometimes I don't think things through," admitted the Doctor, and the soldiers drew weapons. "Now, Jace, I'm no big fan of fighting, but I hear you're handy in a good brawl. Any way you might be able to…?"

"Save our asses?" he finished with a sharp smile.

"Well, yes," said the Doctor.

Jace readied himself for a fight as the Doctor looked on, half excited, half exasperated. As the first of the men drew closer, though, that was a sharp sound, like wind being sliced in two, and the sword the soldier was carrying shot from his hand, flew through the air, and crashed into a wall, shattering from the force of it. All six spun about to see the new attacker, and were faced by a woman.

"I think as far as the Doctor's behind is concerned, I'm the only one with an interest in it," she said, aimed a gun in her hand, and fired again. The soldiers fell back in horror, having never seen a weapon like hers, cast a last, threatening look at Jace and Doctor, and fled.

Jace blinked up at the woman as she approached. She was tall, curvy, with a head full of hair so wild he thought she could be part wolf. As she drew nearer, he saw she had a warm, heart-shaped face, lovely, round hazel eyes, and a pair of full lips, currently moved up in a smile. Jace was about to ask who she was and how she knew the Doctor, but the woman spoke first.

"Hello, sweetie," she said to Jace, and then turned to the Doctor, winking roguishly. "And, _hello, sweetie_."

Jace flipped about to demand the Doctor explain, but he found the man busy slicking back his hair and straightening his outfit. "Who is she?" Jace said loudly, pointing a finger in her direction. "I thought we were going for anonymity here, and suddenly she pulls out a gun?"

The woman laughed and winked at Jace. "I'm River Song, I'm the Doctor's wife."

* * *

Clary was just starting to get anxious when she heard the whooshing of the Tardis. Her heart gave a leap and she rushed toward the sound, followed closely by Amy, Rory, and Vincent. As they rounded the house, the Tardis was materializing. Clary prepared to leap into Jace's arms, but when the door was thrown open, a woman came stomping out, head high, defiance in every line of her body. The Doctor came rushing out after, looking incensed.

"You can't go stealing things, River. It's history!" he cried.

"Exactly. I'm a archeologist, I'm just doing my job. Besides, it wasn't anything important," River said, glancing around and then holding up a scanner. "Hmm, France, 1885. What are we doing here?"

"Nothing important?" the Doctor demanded. "It was the Guttenberg Bible!"

"Ah, well, it's a bit of rubbish anyway, isn't it? _Completely_ out of date with the real world," she said, laughing a little.

"It wasn't out of date then!" the Doctor shouted.

"Time is an illusion," she said indifferently, spotted Amy and Rory, and gave a cry of joy. "Hello, Mum, Dad!"

"Mom and Dad?" Clary asked just as Jace came stumbling out of the Tardis. "You're their daughter?"

River gave Amy and Rory hugs, and turned to find Clary looking up at her. "I am, and you're Jace's little girlfriend, right?"

"Jace?" Clary asked, feeling like nothing was making sense-_again_.

"Yeah, you know Jace. Blond, handsome, temper, not bad with a knife-I like that." River smiled broadly.

"How do you know Jace?" Clary asked again.

"Saved his life, don't think he appreciated it, but then, what's a girl to do when her husband's in danger?" River glanced over at the Doctor. "You never did say why those men were going to cut your head off."

"Nonsense about kissing a man, that's not the point!" the Doctor said, making huge gestures with his hands.

River blinked. "Seems a big point to me, as we're married. Next time you want to kiss a man, let me know."

"River, you're being impossible," he said, coming over and pulling her towards him.

River smiled, all dimples and glowing eyes. "It's what I do best," said River, and promptly, kissed the Doctor.


	11. A Night to Remember

**So, this coming up week is going to be a little more hectic than the others I've had so far. There's still a lot of work left on my research, and a paper, and an exam, so I regret to say, I will not be posting a chapter next week. My hope is that after Saturday, I can start work on this again, and then, that following weekend, the weekend of the 23****rd****, I'll have a chapter posted. Sorry everyone!**

A Night to Remember

_First things first, though not necessarily in that order_

_-The Doctor_

"So, tell me, sweetie, what are you doing with these baby shadowhunters?" River asked. They had said their farewells quickly to Vincent, though Clary seemed to want to say more, and had left. The Doctor seemed to think that River's appearance, coupled with his own, was too much for the history books to handle and had rushed them away, muttering about her nasty habit of taking things that weren't hers to begin with. Now, seated on the Tardis, the Doctor couldn't escape River's bright, sharp curiosity. "Are they really Valentine's Morgenstern's kids?"

"One of them is, though if you ask them, it's always the wrong one," the Doctor hedged. River was brilliant, but the Doctor figured that if River knew the whole truth of the matter, she might rush into action. He wasn't worried for River, of course, it was Valentine Morgenstern who wasn't prepared for what River might do. "Valentine raised Jace, though he's not his son, and Clary hates him, so she's not his daughter."

"I bet family get-togethers are a blast," River snorted. "Why are they with you, though?"

"Well, there was a war, and Valentine wasn't supposed to live," the Doctor said quietly. "He should have been killed indirectly by Clary, but there was a paradox, a mistake in time, and now he's alive. It's bad all around, the Tardis landed and wouldn't let me leave for a month!"

"She wouldn't let you?" River shot the Tardis a considering look. "Whatever is going on with these two, it has to get sorted. Have you figured out what caused the paradox?"

"Yes," he sighed, and then carefully nodded to the other side of the control tower. River followed him, eyes narrowed in their usual calculating way.

"Well," River pressed softly. "What is it?"

The Doctor's eyes were on Jace and Clary who were currently talking to Amy and Rory, Clary, showing off her painting and Jace fingering the small mason jar full of stardust. "It's not good. There was a young boy, Max Lightwood, Jace's step brother, who was supposed to die. From what I've seen, Max didn't die, and this must have caused Jace and Clary to be in the wrong place at the wrong time, thus, Valentine didn't die."

River's eyes were dark. "Can we fix it?"

"I think so, but it'll be tricky. Jonathan was supposed to die too-Clary's older, half-demon brother-" he added, for River's benefit, "But he didn't, and that alone is enough time energy on the loose to tear a nice sized hole in the universe. I'm not sure where to start."

"You'll have to talk to Jace and Clary then," River decided. "Whatever went wrong, they must know what it is."

"And risk telling them Max should be dead?" the Doctor looked outraged. "River, I made a mistake, a bad one. I left them with Valentine for a _month_, and all that time he was torturing them! I should have helped them. I should have stopped him when I had a chance. How am I supposed to just let them know their little brother should be dead?"

"I'm not saying we kill him!" River hissed. "I'm saying we figure out where the time stream when wrong, figure out how to set it right, and save the boy."

"It's not that easy," the Doctor said tiredly. "There's so much that's gone wrong now, what with Valentine alive, controlling the shadowhunters, Max alive, Jonathan alive…It's like everything that could possibly be wrong is!"

"How do we know Max is the reason?"

"Max was supposed to die before the war started," the Doctor said thoughtfully. "Jonathan killed him. Max must be the reason, the point of origin of this mess. There's just got to be a way to fix it all, I'm just not sure how."

River straightened up and glanced over at the children. "Why don't you want to ask them?"

"Life has been tough enough as it is. I thought a few days of relaxation, of fun, of not having to be afraid would help them settle down, but I guess I'm running out of time for this."

"I'll ask," River said decidedly. "I'll be gentle, but I'll ask. We need to know how this all started."

"Badly," the Doctor said under his breath, but allowed River to pass him and join her parents and Clary and Jace.

"Hello, River," Clary said, smiling at the sight of the woman. She had taken an instant liking to River; maybe it was the determination, maybe it was the mischievous look in her eyes, or maybe it was just that her hair made Clary's look tame, but she liked her. "How're things with you and Doctor."

"The same," she said, "holding on by the usual thread. But actually, I've come to talk to you and Jace."

Jace perked up. "About what?"

"It's a bit complicated," the Doctor said, coming upon them and crossing his arms. "Remember the time paradox I mentioned?"

"Something that could consume the entire galaxy if you didn't figure it out?" asked Clary, smiling a little at the memory. Since her time with Vincent and her return to painting, she had relaxed a bit, and seemed happier. More herself. "Did you work it out?"

"I did, but it's a bit trickier than I thought it would be," the Doctor admitted. "Sometimes, with these things, they all intertwine and influence each other, and then to fix one, you have to fix a lot."

"You're not making this much better, Doctor," Amy laughed, sensing his and River's tension.

"I'm sorry," he said, and his eyes were so sad, Clary's smile dropped away and Jace drew her against him. "I'm so sorry, but I need you to tell me what happened the days before the war and what happened that night."

Clary and Jace exchanged looks. "It's not something I like to talk about," said Clary. "It was only seven months ago."

"We need to know," River said gently, and she sat down beside Clary. "To fix this, we need to know where it all started, and to know that, we need you and Jace to speak to us about it."

"Clary," Jace said softly, giving her hand a firm squeeze. "I'll tell them what I know, but parts, only you were there for, and you'll have to tell them."

Clary nodded faintly. "You'll start?"

He smiled in return. "As much as I can."

"Thank you," said River. "I know it can be hard, I know it can hurt, but we want to help you. Jace, do you mind starting just after the first attack on Alicante?"

He shook his head thoughtlessly. "We all arrived back at city circle at different times, from different places. Clary and I were coming back from the Wayland manor house. Alec was returning from the attack with Magnus. And Isabelle was dragging Aline and Max with her." Here, the Doctor and River glanced to one and other darkly. "I think the Lightwoods were there, Luke, and Seb-Jonathan came towards the end.

"He was trying to convince Clary to go off with him when I remembered that Simon was still stuck up at the Guard. We all left, and Jonathan stayed behind, but when we got to the Guard, Simon was almost out, and he had Hodge, our old mentor, with him."

"So, Hodge was alive?" asked the Doctor, hoping that maybe this was really the answer they had been looking for. After all, Hodge was supposed to die then, in a specific way, and if that were wrong, maybe everything that followed was.

"Not for long." Jace looked away, thinking of his words then. "We argued, because I thought he had lied to me. I thought I was…part demon, and that he had known all along. Before he could tell me the truth, though, Jonathan returned and killed him. We confronted him, and he attacked us. After Simon drove him off, we just assumed that he returned to Valentine, but we never knew who he was until Jocelyn told Clary."

"We probably should have guessed," Clary said suddenly, thinking back to that night too. "He was such a good actor, and when he tried to get me away from the rest of the group, I should have known. Was that it?" Clary sat up straighter, excited. "Were we supposed to have known Sebastian was Jonathan, or was Hodge not supposed to have died?"

The Doctor shrugged. "Both those things happened the way history says they did. Changing them wouldn't have altered the present this much. There must have been something else."

Jace continued. "We went back to the city circle and it was like hell had broken loose. People were dead, children were missing, hundreds were wounded, and it took us a while to find the Lightwoods again. When we did, Myrse said we were leaving for a manor house just outside the city and would stay there till the mess was cleared up in Alicante. Luke came for Clary, and we went our separate ways.

"After that, it's all a bit of a blur I guess," Jace said thoughtfully. "Valentine's apparition showed up, gave the Clave his ultimatum, and killed the Inquisitor." Jace met the Doctor's eyes. "Was the Inquisitor not supposed to die?"

"No, he died," said the Doctor, and realized suddenly how much humans always wanted more life. Every person who died, it seemed, wasn't supposed to have. It had never been that way for Timelords; when death came, it came. You could accept it gracefully and go willingly, or you could fight it. Either way, though, when you were meant to die, you did. But how did you accept death when life had been given? "What came next?"

"The Clave was in an uproar for a while over what to do. Clary was the one who said we should join with the Downworlders, but no one took her seriously until she came up with the rune to bind us to one and other. But that was after Jocelyn was woken up."

"How did you wake her up?" River asked sharply, wondering what magic Magnus might have had to perform. Summoning a demon to wake her might have been enough to upset the flow of time much worse than Max's life. "Magnus performed a spell, I'm sure?"

"He used the book we brought back from the manor," said Clary slowly. "Please don't say my mother was supposed to die?"

"No, she woke up when Magnus prepared an antidote," the Doctor shook his head. "You woke Jocelyn up, and then what happened?"

"She told us the truth," said Jace simply. "That I wasn't Clary's brother and Jonathan was. That Sebastian must have been Jonathan, and then I decided to go after him." Here, Clary looked oddly pale, as if the pain of the memory was still too much. "It took a while to find the string with his blood on it, but I did, so the night before Valentine had threatened the Clave with war, I visited Clary, stayed with her the whole night, and then left early in the morning. And that's where our stories break apart."

River drew a deep breath. "Tell us the rest of yours, Jace, and then we'll hear Clary out."

Jace pressed his lips together. "I tracked Jonathan to a valley outside Alicante where Valentine, apparently, had raised him. I overheard the conversation between father and son, about the mirror, about raising the Angel, about Valentine's request, about the army that was going to destroy the helpless shadowhunters, and I was about to reveal myself when Valentine left and Jonathan called me out.

"He said he could have heard me a mile away, and made a few snide remarks about me loving my own sister. I told him I knew who he was, and that I wasn't Clary's brother, and he attacked me. I should have been better prepared, I should have had a weapon ready, but I didn't, and he knocked me out. When I woke up, I was tied to a stone in the cave and Jonathan was summoning demons. I figured I could try and buy time for the Clave by getting him to fight me, so I told him he was a coward and Valentine wouldn't forgive him for it."

Jace looked very bitter, very angry then, and he pulled his hand out of Clary. "It was me, wasn't it?" he asked softly. "I was supposed to stop Jonathan, and then go and stop Valentine, but I couldn't. This is all my fault."

"That's not true, Jace," River said kindly. "What happens, happens, the fact that it didn't, doesn't mean it wasn't meant to be. Keep telling us what happened."

Looking sadly at Clary, Jace said, "I'm sorry, Clary, for everything."

"It wasn't you," Clary said firmly. "I was the one with Valentine. I should have stopped him."

"You can't think like that!" cried the Doctor, jerking himself off the controls and jumping into frantic, neurotic action. "Between every minute, between every _second_, there are a thousand possibilities, a thousand chances, a thousand futures; I know that because I'm a Timelord and I see them all. But, you have to understand, these futures, they're all equally valid, no one is better or worse than the other; they simply are. To say that you did something wrong and ruined the universe is impossible, because, let's face it, you're not strong enough or important enough to change the course of the universe. You changed _your _future, that was all, and who knows? Maybe people who should have died, lived, and maybe people who lived, died. It's all just a big ball of possibilities, and we don't get to pick and choose the best course. These things just happen, regardless of who tried to change them."

"Not for you," Jace said, a tinge of jealously in his voice. "You're here fixing everything. You get to pick and choose."

The Doctor's face dropped and for a moment, he was oddly distant. "There was a time I thought I could change the universe, too. I even tried to change things that can't be changed. It's how I got the name Timelord Victorious; I thought, because I was the last of my kind, the laws of time and space were mine. But I was wrong." He saw River looking at him, completely confused. "It was before you're time, River, before a lot of people's time. The point is, time follows its own laws, and not even I can say for sure, what should happen, because I've been wrong before."

"What happened?" Clary asked quietly.

The Doctor shrugged, but all he said was: "Some people died and some people lived."

Jace wondered what it must be like to have so much power, so much influence, over all life. He had believed for so long now in the absolute power of angels and demons, that he had forgotten how little credit he had once given them. And more to the point, if a man like the Doctor existed, could it mean that all those angels and demons were nothing more than people like him?

_What did he say? I have fought angels and demons. I have held the fate of the universe in my hands? _Jace shuddered. _Maybe there is no god, maybe it's just men like the Doctor. _

"Jonathan and I fought," Jace finally said. "And he got the better of me; I think he almost killed me, but I suspect Valentine had given him strict orders not to. I struggled, I did everything I could to distract him. I hoped Alec might come, just to help, but I realized that if someone did come, they would probably die, so it was better off that way. After that, I let Jonathan have his way."

Jace looked wanly to Clary. "Jonathan brought me to the lake, and Valentine was there with the Angel, and Clary was tied up, too. I thought Valentine might have killed her at first, she was so pale, but he had only used her blood. Jonathan left me with Clary, and we had to watch while Valentine raised the Angel."

Jace didn't speak, whether from shame at his loss or awe of the angel, the Doctor didn't know, and Rory gave Jace's shoulder a reassuring squeeze. For once, Jace accepted the gentle gesture, even enjoyed the feeling of someone understanding his pain, and Rory was glad to see a little color return to the boy's face. Clary, beside him, kisses his cheek gently; she alone knew what it cost him to speak of these things, and realized if someone as torn as Jace could tell his story, why couldn't she?

"When Jace left," she began, drawing his gaze to hers, "I was a wreck. I wanted to go after him, but my mom wouldn't let me. She practically locked me in a room with Isabelle in the manor house they were staying in, and made Alec swear on the Angel to keep me there. It was one of the worst days of my life, really. We didn't know if the Clave would fight, and our families die, or if they would surrender and we'd be slaves to Valentine. Of course, all I cared about was Jace, but Isabelle, Max, and Alec were always more conscious of the greater good. They knew there was more at stake than Jace.

"Towards evening, though, Alec was called away by the Clave, since he was eighteen. Isabelle had sworn on the Angel as well to stay with Max, and she couldn't justify taking him with her. She let me go though, and I made a portal as fast as I could to Valentine.

"When I got there, he was ready to summon the Angel. I couldn't control where I would land when I portaled, and I ended up in Lake Lyn; Valentine fished me out, he saved my life, but he only wanted me to complete the ritual. He told me how much he hated me." She saw Amy's eyes widen. "It's not like I cared all that much, I hate him, too. But then he told me he was going to summon the Angel and I had to watch. He used the Soul Sword, and he cut my wrist across the vein. I thought he would kill me, but he just laughed.

"He said, 'There's no point taking the life of my own blood, especially when I have so many uses for it. Jace will be extremely pleased to see you're not dead,' and then he began mixing everything together in the lake. I was trying to move, to break the circle of runes he'd made in the dirt, but as I was crawling there, Jonathan arrived with Jace.

"I was so happy he was there, and so scared he was dead, I couldn't move. Valentine turned, saw what I was trying to do, and dragged me back to a fallen tree. He tied me and Jace to it, and Jonathan stood guard while he completed the ritual.

"He summoned the Angel, it granted his request, and then it was over. I could feel this strange pressure, on my wrists and ankles, and Valentine told me it was the binding the Angel made, and that I had to serve him now. Jace struggled too much, though, so Valentine made him drink something." She glanced at him and Jace just scrunched his nose at the memory. "He passed out and Jonathan took Jace. I had to ride with Valentine, and we went back to Alicante.

"When we got there, most of the shadowhunters were sick. A lot of them were doubled up, and they were vomiting and convulsing and screaming. Valentine made them all drink from the cup, but only after they agreed to be marked with a permanent binding rune." Here, Clary turned her wrist over and revealed a mark burned into her skin by the force of a white hot blade. "We all got one, and when he found my mother. I think he threatened to hurt me in the end if she didn't drink from the cup, so she did it, and it changed her. It's like she's all empty now, like she forgot everything wrong with Valentine and started right where they left off."

Clary shuddered. "After that, we left. Valentine took Jace, me, and my mom back to the city and he kept us in a cell for a little bit. But after a few days, he made me draw up a portal, and we went back to New York. He told Jace and I that we weren't allowed back to Idris until he let us, and, since he's branded us with the obedience rune, we don't have a choice. We can't go back."

Clary heaved a great sigh when she was done, and carefully looked anywhere but at the eyes of the people watching. Amy, sensing her discomfort, clapped her hands together. "Well, that wraps things up rather nicely, doesn't it? Clary, Jace, do you two want to help me make some dinner? We should leave the Doctor to mull things over."

Jace seemed to want to stay behind, only because there was something very troubling about the look the Doctor currently wore. He was used to bad news, used to learning and seeing horrible things, and he figured whatever the Doctor had to tell him couldn't have been that bad. "I think it might be best if we stay."

"Not at all, Jace," said the Doctor, jumping like he'd been stung. "River and I are only going to talk about all those boring things adults talk about: house, money, cars…mortgage."

Clary saw Jace raise his eyebrows in disbelief, but she tugged his hand a little. "Come on, Jace. Rory did promise he'd show you how to cook a burger, and there's no way we could ever live together if you can't cook me a burger."

As always, Jace went through a minor debate in his mind: stay at the heart of things or tend to Clary. Clary usually won out, and this time was no exception. "Alright, alright, but none of those crummy turkey burgers. It's like cardboard in your mouth."

Clary smiled and she and Jace followed Amy and Rory out. The Doctor waited until the group had gone and then turned to River. She wasn't looking all that pleased either. "How bad is it?"

"Bad." The Doctor began his usual pacing, running through his thoughts aloud. "Jonathan was supposed to kill Max the night the demons entered the city. Isabelle, Aline, and Max stayed behind at the house while Alec went up to the Guard. Aline was attacked by a demon, and Isabelle went after her, so by the time she got back, Jonathan had already returned and murdered Max."

"How did the boy die?"

"Hit over the head with a hammer. Internal bleeding." The Doctor swung about, running his hands through his hair. "It's all a mess. If Max had died, Isabelle would have blamed herself for it all, gone into a deep depression, and stayed that way until she and Clary argued over Jace going after Valentine. Do you remember when Jace said he hoped Alec might come and help him?"

River snapped her fingers. "It was an echo of the alternate reality, wasn't it? At that same moment in another reality, Isabelle came to help Jace fight Jonathan."

"Exactly," he said, letting his breath go in rush of air. "Since Isabelle _didn't_ come, Jonathan overpowered Jace and Jace couldn't kill him-explains why the boy is alive now-and then they both went to Valentine. All this time, Clary was at the lake, just like in the other reality, but Jace was supposed to arrive, confront Valentine, and then Valentine killed him. Clary was so broken and so furious, she broke the ring of runes-like she was trying to do here-and Valentine had no protection against the angel."

"What about the angel?" asked River. "I mean, the amount of energy it took to get that thing here, not to mention the energy it used to enslave the shadowhunters, how did that work itself out? The energy had to be used some way in the alternate reality; if it hadn't, forget the paradox, we'd probably have a miniature black hole on our hands right now."

"After Valentine died, the angel offered Clary one wish, and she asked for him to bring Jace back." The Doctor looked thoughtful. "But that's not enough, not nearly enough. Where did the rest of the energy from that burst go?"

"Another event?" offered River. "What happened after this war that Jace was involved in?"

"Ha!" he gave a hollow laugh. "Jonathan was brought back from the dead by Lilith, disguised as Max in Jace's dream, and used Jace's blood to bind him here. That was a few months worth of hell, I'll tell you that."

"That must be it then," River said after a beat. "Jonathan is not dead, so he can't be brought back, and the war that would have followed must have been worth all the energy the angel put into enslaving there shadowhunters now."

"Like I said, it's a mess. Max lived, but now Valentine is in control. However, had Max died, we'd still have a war with Jonathan to counter. In this case, Valentine was the lesser of two evils."

River massaged her temples and closed her eyes in thought. "How do we resolve it, then? We can't kill Max and we can't kill Jonathan, because either way, it ends with this huge war."

The Doctor looked uncomfortable. "I've never been a fan of killing, River, and you know that. Maybe we can offset the paradox another way?"

River glanced around hopelessly. "It's demons that are causing the problem, maybe if we just remove the demons, we can try to offset the damages of the paradox?"

"Remove the demons…" the Doctor mused, rubbing his chin. "I like it, River, I like it a lot!" He spun around on his heels, kissed her, and made for the stairs. "I'll get Clary's help; she can design a portal rune, I'll enhance the strength by siphoning energy from a black hole, and then use the Tardis to direct the portal to a tear in time. Send the demons back through, close the tear, no more demons _ever_!"

River, used to the Doctor's sudden change in moods and forgetfulness, ran after him, catching him on the stairs. "What about Jace and Clary? What do we tell them?"

The Doctor blinked, considering. "For now, we'll say nothing. Only that we must have missed the paradox and maybe something else unrelated to them caused it. They're only children, after all, and they need a little bit of time to take things in. It's better I let them relax and heal now, give them time to grow into the idea."

* * *

Later that evening, after dinner, after Jace and Clary had thanked everyone-especially the Doctor, who had told them they had nothing to do with the paradox-after Amy and Rory had shared a bottle of wine with River and gone off, after River had kissed the Doctor and told him she'd be waiting in their room, did the Doctor settle before the screen over the controls of the Tardis and scan the readout. His and River's plan had to change the future, but by how much, he was curious. As he expected, the history had changed and Valentine's victory was recorded, but he scanned past that to the end.

"Demon race inexplicably vanishes…Torchwood shows up…Valentine imprisoned…miraculous medical treatment for Jonathan-I'm brilliant-and what else…?" The Doctor read down farther and farther, searching for that one sentence, that one word. "They had to get married," he muttered to himself. He was just starting to suspect that it never happened when he came across Jace and Clary's name in the last entry following the survivors of the Mortal War. "Impossible…" he whispered.

"_**In the year 2014 Jace Lightwood and Clarissa Morgenstern-Lightwood (engagement was confirmed) disappeared and were never seen by family or friends again. Isabelle and Alec Lightwood confirm that the two left Taki's Diner together, and that, as they followed the two down the street, Clarissa turned away and Jace followed. A cry was heard, but by the time Mr. and Ms. Lightwood arrived, Clarissa and Jace were gone. Though their bodies were never recovered, the Clave honored both of them for their courage and help during the Mortal War by burying empty coffins in the Silent City. Their death was counted as one of the greatest losses the shadowhunter community suffered in the 21**__**st**__** century**_."


	12. Rescue

**I'm back! I hope the extra week wasn't too much of a wait, but now my summer is open and I should be able to get these chapters out once a week. I hope you enjoy this chapter and think it was worth the wait. Hope to hear from you!**

Rescue 

_Everybody knows that everybody dies, and nobody knows it like the Doctor. But I do think that all the skies of all the worlds might just turn dark if he ever, for one moment, accepts it. _

_-River Song_

"Where are the Lightwood brats?" Valentine stormed into the Institute, his eyes flashing dangerously in the candle light. Rushing up to meet him was Malachi, face, the picture of worry. "Bring them to me now."

"Sir?" asked Malachi, confused.

When the war had been decided, Valentine had placed Isabelle, Alec, and Max in the care of Malachi. He had been about as pleased by this arrangement as the children had been, and had promptly marked them up with permanent runes, binding them to the Institute. Once a week, he would receive reports from the instructors about the progress the children made, and aside from dishing out any punishments, would rarely seek them out. It was accepted between the Lightwoods and Malachi that they hated each other, blamed each other for their current, unfavorable state, and would only be happy with the other one gone. Malachi, of course, didn't see what value the Lightwoods had, and was surprised to hear that Valentine wanted them,

"The _Lightwoods,_" Valentine hissed through clenched teeth. "Three children: Alexander, tall, dark haired, Isabelle, a pretty girl your eyes were only too happy to follow, and Maxwell, a small, bespectacled boy. I put them in your care. Now, where are they?"

Malachi blinked and pointed upwards. "I think they're in the library studying; at least, that's where I find them whenever I go looking. What has happened?"

"I need a little encouragement," was all Valentine said before he took off for the stairs and the library, Malachi in tow.

Upstairs, Isabelle was seated at a desk, pouring over a text on greater demons; Alec was studying how to make stele blades last longer; and Max's head was bent, his finger frantically tracing a line in a book. First and foremost in their minds was their fear for Clary and Jace, and their desperate hope that had been woken by the strange pair. Even now, they wondered if Amy, Rory, the Doctor, and their friends were on their way to collect them. Every once in a while, Max would lift his head and glance out the window, wondering if some huge, time traveling spaceship was going to fall out of the air and land before the Institute. As they tried to focus on their work, the door to the library was thrown open.

Alec's head shot up and his hand shot out to collect Max to him and Isabelle jumped to her feet. They drew together, standing at attention, waiting to see who had come after them this time. When they saw Valentine approaching like an unwelcome shadow, they fell back. Isabelle wrapped her arms around Max, and pushed her behind him. Valentine came before them, bearing down upon the children.

"So, Lightwoods," he said, smiling down on them unkindly. "I've just received the most interesting phone call, from the _most _interesting man, and I find that I have lost something."

Isabelle and Alec were both thinking the same thing, and knew that if they mentioned Jace or Clary, it would be too much a giveaway. Instead, Alec cleared his throat and said, "What was that?"

"I think you might know," Valentine said evenly, but Alec's face remained the same. "Or perhaps you pretend not to. Tell me, when was the last time you heard from my daughter or Jace?"

"We haven't," said Alec quickly. "Not since the Mortal War, at least. Have they gone missing?"

"You know they have," snarled Valentine, and his towering figure was suddenly very imposing. "You two were Jace's closest cohorts, his little secret keepers. I know he told you where he was running off to. Tell me."

Isabelle opened her mouth to argue, but Alec cut her off sharply. "We don't even know where you took Jace and Clary, and there's no way we could have contacted them, Jonathan and Malachi keep too close an eye on us."

Valentine's grey eyes showed not the slightest interest in what Alec had to say, and Isabelle, sensing this, stepped forward. "Listen, we haven't got the slightest clue where Clary and Jace went. You haven't let us lave the Institute in months-"

"Isabelle!" Alec cried, but she kept going furiously.

"If we had some way of communicating with the outside world, don't you think we might have tried to find our parents? I love Jace and Clary as much as I love my brothers, but I have no doubt running after them is impossible. Wherever your children are, they aren't with us."

Alec's mouth was slightly ajar and his hands helplessly groped at Max's shoulder, pushing him back. Valentine, for his part, was impressed by the young girl. He'd always suspected that one of the Lightwoods must have inherited Myrse's temper, and now it seemed, he'd found out who. Smiling a slightly crooked smile, Valentine leaned a little closer to Isabelle.

"You might be telling the truth," Valentine mused, staring into Isabelle's eyes until she glanced away angrily. "Jace and Clarissa may not be with you, but that certainly doesn't mean they won't come after you."

"Breaking into the Institute is impossible," said Alec swiftly.

"I suspect my daughter and Jace have enlisted the help of someone who might be able to do just that. I'm not so sure I trust these walls," said Valentine, and then glanced around, displeased. "However, I trust Jace, I trust him as much as you do."

"What do you mean?"

"He's always tells the truth, always clings to his loyalties, always wears his riotousness on his sleeves. Jace could never abide his loved ones suffering while he was free and unharmed. He would come if you were in danger." Valentine straightened up and his eyes darkened. "You must realize what this means?"

Isabelle lifted her chin in a challenge. "I'm not afraid of you. If Jace and Clary really are free, and they really do have help, they'll come after us."

"I'm counting on it," returned Valentine in a low voice, and then turned and called back, "Malachi, bring your wards along and we'll make for Idris. It's high time I got my hands back on Clarissa and Jace."

Isabelle and Alec exchanged dark looks and Alec scooped Max up. "Where's he taking us? What about Jace? Are we leaving the Institute?" Max's questions poured out in a low stream into Alec's ear. The idea of finally escaping from the Institute, of possibly seeing Jace, had woken in him a frantic energy.

"I don't know, Max, and be quiet," Alec hissed just as Valentine turned about to shoot him a look. "Just stay by me or Isabelle, don't speak, and be brave."

Max's face changed to one of concern and he nodded quietly. His big eyes peeked out at Valentine who was leading them down the stairs to the entrance hall of the Institute, muttering to Malachi. Max had rarely given thought to the man who had raised his hero, Jace, and even now, found it had to connect his brother to this man. More often than not, he saw Valentine only as the man who had taken his parents and condemned him to life in Malachi's shadow. He frowned just a little, and felt a leaf of fear unfurl in his chest, but set his will firm. Jace had been raised by this man so why couldn't he, Max, be brave about him?

"We're leaving the Institute?" Malachi asked aloud, still confused by Valentine's sudden appearance.

"We're going to Idris," Valentine announced.

* * *

"Where do we go from here?" Clary asked the Doctor softly as they sat over dinner the next evening. "If you don't know what caused the paradox, can we do anything?"

The Doctor's eyes darted to River, but he cleared his throat. "River and I talked, and we think the best thing to do is to put a stop to Valentine in general."

Jace stirred, his eyes glowing with an old excitement Clary hadn't seen in months. "We're going to fight Valentine?"

"Well, we're going to in a roundabout sort of way," shrugged the Doctor. "I don't know if it's completely safe to remove Valentine, and besides, I'm not one for killing. I want to take his power away."

"How do you think we should do that?" It was Amy, and she was intrigued, as always, by the Doctor's ingenuity.

The Doctor grinned boyishly. "Where does Valentine draw his strength?"

"Runes?" offered Clary.

"The Clave," said Jace.

Rory considered it all a moment. "The Mortal Instruments."

The Doctor pointed at Rory. "I always knew there was a reason to keep you around, Rory. Right, Valentine is using the Mortal Instruments to summon and control demons, and he uses the demons to force the Clave's hand. If we take away the demons, we remove the threat Valentine poses to the Clave. Take that away and he's helpless."

"You want to remove _all_ the demons in the world?" Jace's eyebrow was raised. "You realize how impossible that is."

"I like the impossible," answered the Doctor. "If Clary creates a portal rune, I can magnify it using the spare energy from a black hole, and then the Tardis can direct it to the nearest tear in space. You send the demons through there, and there's no coming out."

Clary blinked. "I-I haven't made many runes lately. The last one was…not very angelic."

"I saw," said the Doctor, and he was smiling all over. He jumped up and dashed around, looking for a piece of paper and pen. When he returned to the table, he scribbled on it, looking proudly down on his creation. "This is what you drew." He brandished the design of the rune at Clary and Jace, whose jaws dropped.

"How did you know-?"

"How did she do it?" asked River loudly, shooting Clary an impressed look.

The Doctor winked at Clary. "She probably didn't know what she was doing when she did it. Valentine asked her, and she drew; the Tardis picked up the signal. Well, you can imagine how shocked I was to see this…" He laughed and River shook her head, rolling her eyes.

"Rather impressive, Clary," River whistled. "I thought it was just me and the Doctor who could write Gallifreyan, let alone read it."

"Gallifreyan?" asked Clary, confused.

"The language of the Timelords," said the Doctor swiftly. "It's the oldest language in the universe, the most powerful…you could raise and crush whole galaxies with it. But it died a long time ago." The Doctor's face suddenly dropped, and his eyes closed off.

Clary and Jace shared a look. "If Clary can't read the language, how did she make the rune?"

"No clue," murmured the Doctor, "but it's useful if that's how you're going to be making your runes. I can show you a few useful symbols and you can work them how you like. We need a rune to transport them, but don't worry about the strength, I'll take care of that."

Clary still looked uncertain. "I don't know if I can," she whispered. "It worked last time, but…the other times I tried it went wrong. Horribly wrong."

"What happened?" asked Amy gently.

She shrugged helplessly. "They just were…_wrong_. I tried to mark myself and runes made me really sick, and it burned, and I don't know if another one will work."

"You said the last one you made worked," urged Rory.

"I was scared," Clary said and her eyes found Jace. "Valentine said he was going to hurt Jace if I didn't create the rune. I didn't have a choice."

Amy and Rory frowned and Amy felt a new wave of hatred for the man who had scared his own daughter. She reached out and took Clary's hand. "But now things have changed, haven't they? I saw you painting with Vincent, and I've seen some of your work recently; you're a wonderful artist. It should be natural for you."

Clary smiled faintly. "I have been painting more since I saw Vincent."

"Maybe," offered Jace, "it would help if you had your friends and family around you again? Do you think if the Lightwoods were here, you'd have an easier time designing a rune? Or maybe Luke?"

Clary knew Jace wanted the Lightwoods back, and even though Luke's presence might have been more welcome, she wanted Jace to be happy again. Her eyes found the Doctor. "Can we get the Lightwoods?"

"Of course," said the Doctor, glancing around to River. "The Tardis can trace the signal given off by Isabelle's necklace, and we can break them out."

"Even if they're in Idris?" asked Jace at once. "There are wards around Idris, protective spells to keep people out. Can the Tardis even land in Idris?"

The Doctor laughed. "Please, Jace. The Tardis travels through space and time, and you're asking if it can break through some barriers around a city? I mean, it's got a perpetual _supernova_ as its engine!" When Jace continued to stare at him, the Doctor rolled his eyes and sighed. "_Yes_, Jace, the Tardis can land in Idris."

"Then let's do it!" said Clary, standing up and looking around the table. "I mean, it's going to be dangerous, trying to get past my father and Jonathan, but you can fight him, can't you, River?"

River's eyes gleamed and her smile was wide. "Well, I can certainly show him and thing or two. Do you think it will come to that?"

"One can only hope," muttered Jace.

"Doctor, can we go now?" Clary turned to the young man, who seemed to be considering many things at one time. When he bit his lip, uncertain, Clary clenched her hands into fists. "Doctor, please, I've been worried sick about Alec, Isabelle, and Max for months, every since my father took them. Even now, he could be doing horrible things to them, and even if it will never have had happened, I don't want to wait."

The Doctor looked away but held up his hands in defeat. "All right, but we've got to get a few things very clear, alright?"

"Anything," breathed Jace.

"I don't want you two getting caught up in anything with Valentine; he's still looking for you, and he'll go to no ends to get you. If there's any risk at all, you two have to stay in the Tardis. Also, we're going in to rescue the Lightwoods, and that's _all_." His eyes went from Jace to River. "I don't want a fight breaking out. I just want to get these three, get on the Tardis and fly away. After we have the demons gone, it'll be another thing, but until then, I don't want any fighting. Is that understood?"

Jace raised an eyebrow. "And if we see a fez?"

"Well of course you pick it up," said the Doctor, exasperated. "That's just obvious, isn't it?"

With that, they left the kitchen and headed for the control room. Jace's stomach was in a ball of nerves as he thought of seeing the Lightwoods. They were his family, after all, the people who had taken him in after years with Valentine. Valentine had been dropping cruel little hints that the Lightwoods might be in danger, that even the slightest misstep on Jace's part would result in them being hurt. Besides Clary, Isabelle, Alec, and Max had been the only thing Valentine could use against Jace. His moment of redemption was finally within reach, and it started with the Lightwoods.

The Doctor was fiddling with the controls of the Tardis, sending out its sensors for the telltale sign of Isabelle's necklace. The Tardis groaned in response, but she was searching. "Come on, sweetie, come on," the Doctor urged, rubbing the screen. "I know you can find them; find Isabelle Lightwood."

The Tardis jerked forward and Amy gave a shout. "What's going on?"

"She's found them!" cried the Doctor, ecstatic, and gave a whoop of joy. "Here we go!"

Before Amy could shout back the Tardis began shuddering, and then slamming back and forth, the innocent people inside, holding on for dear life. Lights were flashing everywhere and Clary had to close her eyes and concentrate on breathing to stop herself losing her dinner. The Tardis flipped upside down like a roller coaster and then began spinning like a top.

"What's wrong?" Jace called, having never experienced a ride like this in the Tardis. "Is it Idris?"

"We're going to slam the barrier!" The Doctor sounded ridiculously happy for such a terrifying prospect. "It's going to _shatter_."

"You're insane!" Clary screamed back, and Amy was thinking that Clary had no idea what she was talking about. "We'll die!"

"No we won't," laughed the Doctor. "Come on, sweetie, send that shield to oblivion."

For one long moment, they continued shaking erratically, and then the Tardis crashed headlong into the barrier around Idris. The lights within the Tardis flickered dramatically and she groaned louder than ever, but the Tardis was still lurching forward. And then, with a burst of green light, the Tardis shot like a bullet out of a barrel. They were moving again, and this time, faster than before. Jace could only assume the Tardis had broken the protective barrier around Idris and was now crashing to earth.

"We're landing," roared River over the sirens in the Tardis. "Is there room for the Tardis?"

"We're about to find out," chimed in the Doctor, and he seemed pleased.

Clary and Jace did seem a little worried, and they looked over to judge Amy and Rory's faces. Amy was looking annoyed but unconcerned and Rory kept shooting the Doctor uncertain eyes. "Jace, what if the Tardis materializes in front of Valentine or Jonathan?"

"The Doctor said they couldn't get in…" he said uncertainly.

"What if it lands on Isabelle?" gasped Clary, thinking a number of horrible things.

Jace grinned wickedly. "Well, in that case, I don't have to get her a birthday gift this year, do I?"

"Jace!" Clary cried, but the Tardis was now shaking so hard Clary was vibrating and her words were slurred. They were about to land.

* * *

Isabelle tugged the chain around her wrist uselessly and glanced at the door warily. She was waiting, tense and ready to pounce, on the door to open and reveal their attacker. Valentine and Malachi had marched the Lightwood siblings into the Guard and down to a cell where they bound them in chain. Malachi had glanced back once at Isabelle with a dark, calculating look in his eyes, and she knew, terror rising in her throat, that if Valentine killed Alec and Max, Malachi would take her back to the Institute…

_And then what? _asked a small voice in Isabelle's mind. _You saw the way he looked at you, you know he's been watching you lately. _Isabelle cringed away from the idea. _Maybe you can get Malachi to save your brothers from Valentine if you…well, if you give him a good flirt._

Slowly, Isabelle's eyes moved to her brothers, sitting on the bench chained to the wall. Alec was slouched, looking miserable and Max was cradled in his arms. The little boy looked up through Alec's arms, his eyes magnified by his glasses, and he blinked slowly. While Max had been spared most of the punishments, Alec hadn't been quite so lucky. He had a nasty bruise over his eye where Jonathan had hit him a few days ago and his wrist was bleeding from the chain. He looked scared.

"Alec, do you think Jace and Clary escaped with that man-the Doctor?" she asked faintly. "Maybe they are going to come for us."

Alec shifted the weight of Max around and tried to sound hopeful when he felt miserable. "It's possible, I mean, Amy and Rory were very nice and they said he could help."

"I wonder what it's like to just be able to leave like that." Isabelle smiled at the idea. "If you're tired of place, just get up and go."

"It must be nice," was all Alec said. He was thinking how nice it might be to go now, since he knew that very soon Valentine was going to begin hurting them. Max was a little boy, and he hoped Valentine might spare him, but Isabelle was a fine age, almost an adult. "It could really help us."

"Don't think like that," said Max loudly. "Think about Jace and Clary and fixing everything. If the Doctor really does stop Valentine, won't all this be…well, will this never have happened?"

Isabelle and Alec shared a glance just when there was a strange rushing sound, and a high wind picked up. Isabelle's hair was whipped around and Alec jumped to his feet, almost pushed back by the force of the thing. There was an echoing all around them and Isabelle wondered if some demon was forming before them; she readied for an attack as something began to form, fading in and out.

"What is that-?" began Isabelle, but the air blowing around filled her mouth and throat.

Before the Lightwoods was a large blue box. They saw the light on the top of the box, flashing like a warning, and a blank window giving them a view into nothing. Across the top of the box were the words: Police Public Call Box. Isabelle drew a bit nearer, confused, and at her side, Alec stared open-mouthed. The wind faded and the room fell silent, and the police call box rested.

"What's a police call box?"

"Isabelle!"

Clary came bursting headlong out of the box, her eyes bright and open, a smile wide on her face, and her hair billowing out behind her. Jace came tumbling out after her, trying to reach out for her arm at the same time as he was running for the Lightwoods. A number of other people came stumbling out after Jace and Clary: Amy and Rory, a woman with a head full of curls, and a young man with glowing green eyes. There was a general pause and then the voices broke through.

"Jace!"

"What are you doing here-?"

"Alec, are you alright-?"

"What's that thing-?"

"Get in the Tardis-!"

"How did you get here-?"

"Who are they-?"

"Get in the Tardis-!"

"Is that the alien-?"

"We don't have time-!"

"Are we in Idris-?"

"_GET IN THE TARDIS!_"

It was the Doctor who finally managed to silence the onslaught of questions. He was looking a little shaken with his own outburst, but it had had the effect he'd wanted. Everyone turned around to face him, looking guilty. Isabelle raised an eyebrow and lifted her wrist for everyone to see.

"I don't know what a Tardis is, but I'm not getting in anything with my hand chained to the wall. You think you can break a binding rune?"

River came over to Isabelle, scanning the chain holding her to the wall. "It's nothing special, Doctor; the metal has been magnetized by the rune. A good blast from the screwdriver will disrupt the magnetic field."

"Who the hell are you?" Isabelle said, not unkindly.

"I'm River Song, sweetie," she smiled, all dimples.

"Alright, alright, make way for the screwdriver," sighed the Doctor, coming up to Isabelle to examine the chain for himself. He pointed the sonic screwdriver at it, Isabelle's eyes staring at him all the while, and then activated it. The chain rattled as the magnetic field was disrupted, and then it fell apart into a hundred little pieces of metal. "Never doubt the sonic."

Alec and Max pulled back as the Doctor drew level with them, but he smiled like a boy, and they relaxed. Like Jace, they could sense something about him was wrong, something about the Doctor was not human. They knew, however, that he had come to help them and they concentrated instead on the idea of freedom. As the Doctor waved the sonic screwdriver over the chains, they too fell apart.

"What is that?" asked Max curiously; he didn't know much about technology to begin with, and this was unheard of in the early twenty first century.

"Sonic screwdriver," answered the Doctor, waving it around. "Useless when it comes to a fight, wonderful at everything else."

"You're the Doctor," said Alec, and it wasn't a question.

"I am, and you're the Lightwoods in need of saving, and here we are, saving you!" The Doctor looked pleased with himself. "Which is why I repeat, get in the Tardis."

"We can't all fit," Isabelle protested, looking at the blue box that had somehow appeared in their cell. "It's impossible."

"The Tardis is interdimensional," answered the Doctor promptly.

"It's bigger on the inside," said Amy to Isabelle's look of confusion. "But the Doctor's right. We really do need to get out of here before Valentine comes back. He's hunting for Jace and Clary as we speak, and probably expected them to arrive any moment."

Alec glanced to Jace, his brother he hadn't seen in months, and felt his heart swell a little. "You came for us anyway?"

Jace shrugged. "It's gonna take a crack team to bring Valentine and Jonathan down. I figured I'd start with my family."


	13. Across the Sky

Across the Sky 

_I am, and always will be, the optimist. The hoper of far flung hopes and the dreamer of improbable dreams_

_-The Doctor _

"This isn't possible," whispered Alec, some time later as he sat in the control room of the Tardis, his eyes restlessly moving from place to place. "How did he fit…where are we…?"

"You sound remarkably like your friend over there," said the Doctor in an offhand sort of way. He had decided he liked the shadowhunters very much, or, at least he found them slightly amusing. They certainly never ceased to provide him with entertainment. "I don't think Jace believed me about the whole thing until we went to visit Van Gogh."

Alec tore his eyes away from the column in the center of the room, pulsating with a strange green light, to stare at the Doctor. "Van Gogh?"

"Yes, very nice man, bit mad, but there you have it." The Doctor smiled dauntlessly and fiddled with the dials on the control. "Then there was our skimerish in old Germany."

"Who are you?" Alec asked after a beat. Alec hadn't given much thought to the man behind the rescue. Distantly, he'd considered what Amy and Rory had told them about his ability to travel through time, but he'd put it from his mind. _Maybe it's better not to think about it? It's such a huge idea…such a vast concept…_Time travel was impossible, wasn't it? How could this man be here? "_What_ are you?"

"I'm a Timelord," answered the Doctor simply. "My people were masters of time and space; we discovered time travel thousands of years of ago."

"And where are you from?"

"It doesn't really matter," said the Doctor gruffly, his eyes dropping away. "All that matters is that I'm here now."

Alec hadn't missed the way the Doctor's eyes had darkened. Unlike Jace, Alec was far more attuned to emotions of others, and he sensed a deep pain in the Doctor. "Why would you come all the way to this planet if you have a home and family?"

"When you make the universe your playground, home is boring," he said with a quick smile, and Alec suddenly lost what little grip he'd had on the Doctor's thought. The man, he realized, was more layered, more complex, than any other creature he'd ever met before-including Magnus. But the thought of Magnus made him ache. "Jace said you were trying to fix what had gone wrong; can you really save everyone?"

The Doctor pressed his lips together, deep in thought. "There's been a glitch in time, a paradox, and the only way to fix it is to try and feed energy into it. See, time is kind of like a set of balances; energy is entered and released with each action. When one action that should have occurred doesn't, the energy that should have been fed into the balance, isn't. This upsets a lot of things in the universe, and it leads to rather unfortunate consequences…"

"Consequences worse than demons flooding into the world and my people being enslaved?" Alec challenged.

The Doctor offered him a mirthless grin. "This entire galaxy and all life in it, consumed by a massive black hole sound bad enough?"

Alec swallowed. "So, you're going to try and fix the scales?"

"Create an event of equal energy and, hopefully, stop the universe from falling apart." The Doctor pushed a few buttons on the Tardis controls thoughtfully. "Sort of par for the course as far as I'm concerned."

Alec blinked once and then looked over to where Jace and sitting with Clary, telling Max a story, probably of their daring escape through time. "Jace spoke highly of you, said you really helped him and Clary out. Are you going to stop Valentine?"

"That's the plan," murmured the Doctor.

"You know he's got an army of demons and half-demon son as a monster?" Alec thought of Jonathan's dark eyes right before he struck out at you.

The Doctor snorted, unimpressed. "Yeah, well, I've got a time machine with a perpetual supernova as the engine. Let's see who comes out on top."

"Alec!" It was Max. "Alec, you won't _believe _who Jace saw!"

"I bet I won't," Alec muttered under his breath, and then turned to the Doctor one more time. "One day, I'll know who you are."

The Doctor's look was one of tired amusement, like he'd met people like Alec before; and maybe he had, but that didn't mean Alec was any less determined. "Maybe one day you will, but I doubt it. Now, go see your brother, Jace has been waiting for you for a while."

Alec preened a little at having Jace likened to a brother, and went to join them. Max was practically shaking with energy. "Jace saw Van Gogh _and _he met Beethoven, and don't we have a painting by Van Gogh in the Institute? He got to see space and he's got star dust in a jar, and-"

"Max, why don't you let Jace tell his own story?" Alec said, catching Jace's eye with a smile.

"Max is doing a fine job on his own," Jace shrugged. "He got all the important parts down, anyway. Besides, I've been a bit interested in what you've been up to more than me."

Alec chuckled. "You travel through space and time and you think _I've _got a more interesting life. You're insane."

"Have you really been at the Institute this whole time?" Jace asked, thinking how close Valentine had been keeping them. He must have thought it was one big joke, probably got a good laugh out of it, watching Jace and Clary coping with the loss of their friends and family only to have them locked up on the other side of town.

"He split us up," Alec began softly, rustling Max's hair. "I think Mom and Dad are somewhere in Idris, probably prison, because they won't let Valentine mark them. He used to say it wasn't going to be a choice much longer, like, he was gonna make them or something."

"He did that with Jocelyn, Clary's mom," Jace said thoughtfully. "He made her drink something, and then marked her, and it was like she had forgotten everything wrong he'd ever done. She didn't even care when Valentine hurt Clary, just thought it was 'all for the best' and told Clary to try to make her father happy." Jace shuddered as he recalled Jocelyn's empty eyes. "He was controlling her, making her see the world through his eyes. I bet he wants to do the same with your parents."

Alec's teeth were bared in a snarl. "If he thinks he can hurt our parents he's got another thing coming."

"Who's trying to hurt our parents?" Isabelle and Clary had returned from the small tour Clary had given Isabelle of the room she and Jace were currently staying in.

Isabelle had always been a straight forward kind of person; what you saw was what you got, as for as she was concerned. When Isabelle had walked onto the Tardis, seen the vast interior and the impossible properties of the ship, she'd swallowed any surprised remarks and asked Clary to show her to a place to sit down a moment. After five tense minutes where every thought in her head screamed that she was mad, where she went over and over her lessons as a child about other dimensions, and where she kept glancing from the Doctor to Amy and Rory and then to Jace, she'd decided it all made more sense than anything else she'd seen lately and she wasn't going to cause problems.

"Valentine," replied Alec gruffly. "I think he might be trying to do the same thing he did to Jocelyn."

"He's going to mark them?" asked Clary swiftly, thinking of her mom. "If he does it'll be like everything he says and does is right, and no matter what you say to them, they won't care." It was hard to miss the bitterness and longing in Clary's voice. "We'll have to stop him before he hurts them."

"So, what's this master plan of yours, then?" asked Isabelle, always one to keep in action. "Are we going to attack Valentine and Jonathan, win back the Mortal Instruments?"

Clary and Jace glanced between one and other and Jace cleared his throat. "Well, the Doctor's got a plan, and it's sort of roundabout, since we're not sure what caused the paradox in the first place."

Isabelle gave the Doctor a long look from where she was seated, and said, "And what's the Bowtie got to say about it?"

Clary snorted but Jace continued. "He thinks Clary can make a rune, a Portal rune, and he was going to…enhance it-somew how-and send all the demons Valentine summoned through a hole in space."

Isabelle and Alec both raised their eyebrows. "He's got a hole in space?" asked Isabelle.

"Well, I think he knows where to find on," said Clary quickly. "This way, with all his demons gone, Valentine and Jonathan won't be nearly so dangerous. It'll give us the upper hand when we go to take back Alicante. He won't have an army, after all."

"And what about Jonathan?" asked Alec. "Your brother's one hell of fighter, Clary. If Jace couldn't stop him, what makes you think the Doctor can?"

"Yeah," said Isabelle quickly. "Besides, how do you know you can trust this man? I mean, what makes you so sure he can actually help us? He doesn't seem all that _dangerous _to me."

Jace and Clary both cast a sideways look toward the Doctor. "He's not what he seems," Jace finally said. "There's something about him that is more than all his silly mannerisms and his bowties and his smiles. I was talking to Amy and Rory, and they said some things about him."

"Things?"

"Like, that he restarted all of time and space," Clary answered. "He made the Big Bang happen."

"And that once, he was supposed to die, and if he didn't, time would die. But, he faked his own death, by dying, and then came back and erased himself from history." Jace shook his head. "I know it doesn't make any sense, but there's more to him than we're seeing."

"Amy said he was soldier," Clary whispered, and her eyes fell. "She said he's the last of his kind. There was a war a long time ago, and she said he was the only Timelord to survive. And all those names he called himself," Clary added, thinking of the phone call to her father.

"He called Valentine," Jace explained, "and he was going on about who he was. He said, the Oncoming Storm, the Destroyer of Worlds, the Predator…"

"I think he can help us," Clary finally said.

Alec pressed his lips together, but there was a look in Jace's eye that was telling him to trust the Doctor. "So, you're going to make a new rune?"

Clary nodded firmly. "I've been thinking about it, and I know what I want to draw…or, I know what I want to _feel_ when I draw. I'll make the rune, and then the Doctor is going to use a black hole or something to make it stronger."

"It's sounds a little crazy," Isabelle hedged, "but I like crazy!"

"By the way," Alec said in an undertone. "Who's that woman who keeps going up to the Doctor and talking to him? I know Amy and Rory, but they never mentioned her. It's just that she's got this look, like she's hunting or something."

Clary smiled, knowing exactly who Alec was referring to. "That's River Song; Amy and Rory's daughter. She's the Doctor's wife."

"He's married?" Isabelle hissed, and Clary saw a frown form her lips.

"Hoping for a hot date?" Jace joked.

"Well," Isabelle said, mulling it over. "It would have been nice to say that I dated an alien. I mean, anyone can date a Downworlder, but a guy from another planet? That's unique. Plus, he's cute."

_Just like you thought Simon was cute?_ Clary thought bitterly, only to be reminded that she didn't know where Simon was. "Isabelle, do you know what happened to Simon and Luke and Magnus?"

She had touched a cold spot for Alec, whose eyes dropped. "Not a clue," Isabelle murmured. "I don't think they're dead, because Jonathan used to tease me about dating the vampire, and he spoke about Simon, but never in past tense. And I think Valentine kept Luke around because he wants revenge."

"That sounds like him," Jace grunted, thinking of the man who had stolen Valentine's wife. "He probably wants to drag out the torture as long as he can. I hope Luke's not in too deep."

"And Magnus?" Clary dared to ask. "Have you heard what happened to Magnus?"

"I think he's in hiding," Alec finally said. "During the war, when I saw how badly we were in, I told him to run. He didn't want to leave me, but I knew if he stayed he'd be killed, so I sent him going."

"So he could still be alive?" Jace asked hopefully. "It'd be great if we could find him, and he could help us fight Valentine and Jonathan once the demons are gone."

"We've got no way of contacting him," Alec said at once. "I've been trying to think of a way for months, just to let him know I'm still alive."

"Well, the Tardis found you," Clary reasoned. "I'm sure the Doctor could find Magnus if you told him."

Alec frowned. "I'm not sure Magnus is first on his list of priorities."

"He's a good man," Jace assured Alec. "If you ask, I think he'll help you out."

There was a moment of general silence where they all looked up hopefully to one and other. For the first time in almost half a year, the Lightwoods were reunited, and there was an inkling of optimism, the idea that Valentine might be stopped. For Jace and Alec, especially, the moment was blissful, as their long separation had become physically painful. As one, they all looked toward the Doctor as he gave his usually whoop of joy.

"Alright gang: Ponds, Lightwoods, Morgensterns, River! Oh! I've got a gang, I've never had a gang before." The Doctor gave himself a congratulatory pat on the back. "Let's circle up and figure this rune business out. We've got an army of demons to send to another dimension and not much time to do it in. Thoughts?"

"Ambitious?" offered Alec, winning him a swift smile from Clary.

"Yes, thank you," said the Doctor, nonplussed. "It's never even the demons I'm that concerned for. I'd like to make sure we're comfortable handling Valentine and Jonathan. Those two will be a handful."

"Leave them to me," said River breezily as she entered with her parents. "I'm sure whatever Jonathan's got up his sleeve is nothing compared to what's up mine."

Isabelle gave River a once over and said aloud, "I'm not sure a Mundane is up to handling Jonathan, especially not one who hasn't got a weapon in sight."

River laughed. "Sweetie, do you know what I'm famous for?"

"Here we go," muttered the Doctor, rolling his eyes dramatically.

Isabelle raised an eyebrow in response and River said, "I killed the Doctor, and I got away with it. I'm the most wanted war criminal in the universe. I make Valentine and Jonathan _and _Lilith look like child's play." River tossed her hair back, reached into her pocket, and emerged with a futuristic looking gun. Isabelle just had time to open her mouth before River fired and the bullet whizzed past Isabelle's left cheek. "I'm River Song and I think I can handle a boy and his father."

Isabelle exchanged a look with her brother and swallowed. "So, you want to fight Jonathan? Aright, he's yours."

"No, he's not," said the Doctor loudly, and River's face turned into a pout. "I'm not sending my wife off to get herself killed."

"Oh, I won't get killed," sighed River. "Jonathan and Valentine are just boys, and I happen to have some very useful Hypnotic Lipstick."

"No. I'm not sending my wife out to kiss other men, either," growled the Doctor to River's glowing face.

"I think the best approach is to first remove the demon threat," Jace said and then his eyes moved to Magnus. "I think it might help if we had a few extra pairs of fighting hands on our side. I hear Magnus Bane has gone into hiding, and if we free Luke and what's left of his pack, we could have quite a force behind us."

"Simon," Clary said suddenly. "I want Simon with us, too."

"Simon as well," Jace agreed, wondering how the Doctor would take it. Was he stepping too far? "If you think we can find them."

The Doctor's look brightened. "Yes, it would be nice to have some people to help contain the situation. It shouldn't be too hard to find the Warlock. So, we need the warlock, the wolves, and the vampire; we'll make a motley lot, won't we?" But the Doctor seemed pleased. "The rune, Clary, do you have an idea of the rune?"

Clary's eyes dropped, but her gaze landed on Jace's hands and she swallowed down any doubts. "I think so. Where am I supposed to draw the rune?"

The Doctor grinned in an odd sort of way. "Across the sky in stars."

* * *

Clary was watching the Doctor as he piloted the Tardis carefully closer and closer to a black hole, when she felt a hand carefully run down her spine. Amy plopped down beside her and gave her a winning smile. "So, you think you're ready for this?"

Clary shrugged hopelessly. "Does it matter if I'm not?"

Amy wrapped an arm around Clary's shoulders and kissed her forehead; Clary, so starved for a mother's love, sank into her embrace. "If you're not ready for this, the Doctor won't make you. All that matters is that you feel comfortable."

"I want to fix what went wrong," Clary finally said. "I've been working on the rune for the last few hours, and I hope I've got it right, but…what if it's wrong all over again?"

"You'll get it right," Amy promised.

"Do you want to see the rune?" Clary asked suddenly. "I've practiced it a couple time on paper."

"I'd love to," she said.

Clary reached into her back pocket and pulled out a folded up piece of paper which she presented to Amy. In the center was the new rune. It was circles within circles, connected by lines. For Amy, it looked like nothing so much as geometric shapes, but for Clary, she saw a portal, a hole in space that pulled things in. Like a black hole.

"This will pull the demons into the tear in space?" Amy asked, holding it at a distance.

"That's what I've meant it to do," Clary whispered. "What do you think the Doctor meant by writing across the sky in stars?"

"I think he's about to show you," Amy said, nodding at the Doctor who was pulling what appeared to be a parking break into check.

"So!" The Doctor clapped his hands together, calling everyone around, and waving Clary up to join him. "I figured the best way to make this rune work is to write it on a larger scale. To really give it a bit of a kick, you know? Now, when I said I would use the Tardis, I meant it mostly as a towing truck."

"Towing truck?" asked Isabelle, confused.

"My people practically invented gravity," sniffed the Doctor. "We're going to use the Tardis to move stars into the pattern of the rune Clary has designed, feeding off their energy." The Doctor smiled to the looks of amazement. "Clary, may I have the design, and will you join me at the controls?"

Clary's eyes moved to Jace who nodded encouragement. "You'll help me?"

"Always," said the Doctor and directed her to the controls. "Now, the screen is showing you a display of the stars around us. I'll help you pull them into the shape you need. Put the rune here, before us, so we can see what we're doing."

Clary placed the paper with the rune before them and she carefully wrapped her fingers around the controls. Beside her, the Doctor was whispering directions into her ear, how to fiddle the controls properly, how to activate the pull. Slowly but surely, Clary and the Doctor moved the stars across the sky into the shape of the rune.

_I'm moving stars, _Clary thought in wonder. _I'm making a new constellation. _It was almost laughable, and Clary thought how much she wanted to tell Simon this.

"Are the stars actually moving?" Clary asked aloud, only able to view small dots on the screen. "I mean, am I actually moving stars across the sky?"

The Doctor laughed. "You just wait and see."

It took maybe half an hour and ceaseless concentration. When it was done, both the Doctor and Clary gave a whoop of victory and threw their hands up. Jace, Alec, and Isabelle were seated together and Amy and Rory had put Max to bed. At their cry, they all rose with a start and their eyes slid to the door to the Tardis. The Doctor rushed past and threw open the doors, giving them all a view of the nearby universe.

Across from them, Clary's rune was twinkling in the sky.

* * *

Thousands and thousands of miles away, in Alicante, Valentine Morgenstern felt a stinging on his back. He gave a cry of shock and then tore the Soul Sword off his back. In horror, he watched as the sword began to fall apart, small pieces of metal chipping off and dusting the ground. Before his very eyes, the Soul Sword disintegrated and Valentine was left with a pile of dust.

"What is this…?" he asked softly.

From somewhere close by, he heard Jonathan give a cry of unbearable pain.


	14. Betrayed

Betrayed

_Do what I do. Hold on tight and pretend it's a plan!_

_-the Doctor_

"It's beautiful," Jace told Clary softly, staring, mouth agape, at the twinkling constellation in the sky. He recalled the stories he'd read as a boy, the Greek mythology about gods who moved the very stars themselves. _A mortal man falling in love with a Greek goddess, that sounds about right, _he chuckled to himself. "Clary, it's more amazing than anything I've seen in my life…imagine what Valentine would say if he saw this. Imagine the look on his face!"

Clary blushed. "It was the Doctor, Jace. He was the one who taught me a few runes of the Timelord language and he was the one who helped me move the stars. He thought of the whole thing!"

Jace kissed Clary's hair. "You made the rune, Clary, you made the most powerful rune that ever existed."

Clary sighed and cast a sneaking eye over to the Doctor. He was, as usual, at the controls of the Tardis, and he seemed to be deep in thought, his fingers moving swiftly over the buttons. He would glance occasionally at the screen, and Clary saw the strange black hole that she knew he was trying to manipulate. "He's a very impressive man, the Doctor."

Jace shrugged. "Yes, I don't deny that; but I don't think I envy him much." Clary gave Jace an inquisitive look and he said, "Well, look at him. He spends his entire life, flying around space and time, getting caught up in the thick of things wherever he goes. It makes you wonder, doesn't it, what type of man does that to himself."

"A sad man," Clary said decidedly. "I think he's very sad and very often lonely. Amy and Rory mentioned the Time War, but they never said what happened."

"I don't think he'd tell us if we asked," Jace muttered. "At least, I don't think he'd tell us now, but we've got a few more important things to worry about than the Doctor's past right now. Isabelle, Alec, stop fawning over the time machine, we've got planning to do!"

Isabelle, who had been deep in conversation with River, frowned at Jace, but Alec nodded over and she grudgingly joined them. "So, what's the next move?"

"I think we need to get Magnus and Luke, at least," Jace said thoughtfully. "Right now, Valentine and Jonathan are probably going out of their minds trying to figure out what we did. In their confusion, we should have just enough time to-"

"Jace," Isabelle said, hands on her hips. "We're in a _time machine_. I think we've got all the time in the world. So, since we've got this time, let's plan this out carefully. We don't want a repeat of our rescue, do we?"

"What was wrong with you rescue?" asked the Doctor loudly. They all spun around and found the Doctor leaning over the railing and smiling crookedly. "I think is went swimmingly."

"If you don't count the frantic, confused fight, then yes, it went fine," sniffed Isabelle.

"Confusion and hysteria are calling cards of mine," agreed the Doctor as if Isabelle had complimented him. "I think they lend an overall _exciting_ element to the experience. Besides, what's life without a little chaos?"

"Much more enjoyable," muttered Alec. He heard someone snort and looked over his shoulder to see Amy and Rory smiling at him; Amy winked at him and he smiled uncertainly back. "I don't know where Magnus went into hiding."

"I'll be able to track him down," the Doctor said. "A warlock of Magnus's status must be giving off pretty powerful electromagnetic waves; like a big flashing light for the Tardis. As for Luke, well, werewolves don't exactly emit tidal waves of energy."

Clary frowned a little. "I want to get Luke away from Valentine; my father hated Luke, so he's probably taken a lot of his anger out on him."

"Luke first then," Jace said, looking helplessly to Alec. "If we can get Luke and Magnus I think we'll be able to pose a significant threat to Valentine. The Soul Sword and Mortal Cup should be useless at this point; his grip on the shadowhunters is merely his control over runes now."

"Then isn't this the time to strike?" asked Isabelle, eyes gleaming. "Shouldn't we be trying to bring them down now before they have time to rally their support? I particularly want to fight an army of shadowhunters, even _with _a time machine."

"I'm not worried about the shadowhunters," murmured the Doctor. "I think we need to render Valentine helpless, since, as you said, Jace, it's only his power over runes that pose a threat."

"And how are we going to go about that?" asked Alec a little more sharply than he intended. "I mean to say, Valentine was no helpless shadowhunter to begin with. He can fight."

"He's dangerous," Jace said solemnly, wishing it weren't true. "He raised me, Doctor, and I know what he's capable of. You'll have to kill him if you want to stop him."

"Dangerous…" muttered the Doctor, eyes racing. "Dangerous, that's the rub…"

Alec considered the Doctor and turned to the nearest companion, Rory. "Is he always like this?"

"No," Rory said thoughtfully. "He's usually much more confusing, saying things like-"

"The Temporal Grace Unit!" the Doctor exclaimed.

"-things like that," Rory finished. "He's a bit absent minded; or, maybe, he's just really well minded and we're the absent ones."

"River," the Doctor was saying. "Can you fix the Temporal Grace Unit in the Tardis?"

"Sure, but why?" she asked, thinking about the complicated machinery she was going to have to fix. "It could take a few days."

"Well, I've thought about it, and here's what I got: Valentine is dangerous, and we need to make him un-dangerous."

"Un-dangerous?" snickered Isabelle, smiling a little at Clary.

"Yes, exactly," said the Doctor seriously. "Let me explain. A Tardis is interdimensional, and this means the inside of the Tardis is in a different dimension than its outside. The dimension of the interior of the Tardis is in a state of Temporal Grace. It means that anything inside the Tardis not only doesn't exist, it is harmless."

"I don't exist?" asked Isabelle, glancing down at herself unhelpfully.

"Inside the Tardis, you don't exist to the outside world," the Doctor said simply. "The point _is,_ if I can get Valentine inside the Tardis, he will cease to exist to the world as you know it. And, more importantly, he won't be able to hurt anyone inside the Tardis. If Valentine doesn't exist…"

"The runes won't be effective anymore," Jace breathed, smiling over at the Doctor. "He won't be dead, so it won't necessarily change the time stream, but it will stop him. That's brilliant."

"My ideas tend to be," agreed the Doctor. "What do you say, River, can you fix the Temporal Grace circuit?"

River glanced down at the Tardis grated floor. "Give me three days and your sonic screwdriver and you've got yourself one working circuit. How are we going to lure Valentine into the Tardis?"

The Doctor glanced over to Jace and Clary. "You two spent the most time with him, you especially, Jace. What will convince him to follow us into the Tardis?"

Jace and Clary exchanged looks. "The idea of getting revenge."

* * *

_Hellfire, that's what it is, hellfire. I'm being burned by hellfire. It doesn't stop…it won't stop…_someone_, make it stop…_

…_please, make it stop._

Jonathan lay trapped in a body, a useless, immobile body that felt nothing, knew nothing, but pain. Every fiber of his body begged for release, but he couldn't speak, and so he remained trapped. Distantly, beyond the pain and the madness that was slowly consuming him, Jonathan wondered how he could have lived for so long and never known this much pain. He had lived all his life with pain as his shadow: his childhood marked by it, his adolescence defined by it, and his actions seeking it-even as a baby, Jonathan had known the sharp pain of a distant mother. But this, this was different.

It seemed to Jonathan that he was being pulled apart from the inside out. His bones were cracking under the grinding pressure of the force, his insides roiling, his blood boiling. Surely,_surely_, this was what it meant to be condemned to hell?

_I must have died, _Jonathan thought faintly. _Something must have happened, and I must have died. I'm in hell now. How very fitting…_But that didn't make sense, did it? Jonathan was part greater demon, he knew, and so his rightful place was in hell. Why would he feel pain like this if he were where he belonged? _I'm only part greater demon; this pain must be the human part of me-the angel blood-that's being torn out. The hellfire is burning out whatever of the Angel is left in me._

It certainly wasn't a happy thought to know that he had finally gone to hell, but it was oddly, darkly, satisfying. In some way, Jonathan was happy to know that he could drop any pretenses of his angel-self. He had lived a long while now, lying to anyone who asked, and, more recently, to all those empty-minded shadowhunters. Now, he could stop pretending and be what he was born: a demon.

_Relax, let the Angel be burned out…relax and let what must happen…this is what you want…_

_Isn't it?_

This last thought burned through Jonathan like the fire that was eating him alive now. Certainly he wanted to become a true child of Lilith, didn't he? Jocelyn wasn't his mother, she had betrayed him when he was but a baby, and he turned away from any decency then. He should just accept this as his fate and reach his fullest potential. But, for some reason, Jonathan couldn't let himself go. For some reason, he was…

_Scared. I'm scared to let go. _Jonathan tried to force himself to let go of the goodness in him, but some unnatural, unreasonable part of him fought back. _I don't want to be a demon…I don't want to be damned. I don't want to say goodbye to the light of the sun and wind in the grass and the starlight in the night. Someone…don't let me go yet._

But still the fire raged through him and Jonathan wondered if he might just be trapped like this forever. The demon part of him wanted release, but there was a small part of his soul that still belonged to the Angel, and that was clinging desperately to life, and so he was trapped in this purgatory, unable to go forward or back.

_Make it stop…make it…_

"Stop," Jonathan groaned aloud. The sound of his voice stirred to life the woman who was asleep in the chair beside his bedside. "Stop."

Jocelyn sat up straighter and lurched to the bed, taking Jonathan's hand in her own and rubbing. His hand was hot, as if a fever was blazing through him, and there was sweat pouring down his face. Terrified, Jocelyn undid the buttons on Jonathan's shirt and tugged it off his body, it came away covered in sweat and his skin shone in the candle light of the room. Jonathan's chest rose and fell hectically, and when Jocelyn listened for his heart beat, it was erratic. Petrified that he might be having a heart attack, Jocelyn wrung out a rag and wiped the sweat off while she called for help.

"Jonathan, please, it's okay; I'm here, your mother is here," she cooed as a nurse rushed in and checked his pulse and temperature.

The nurse cast Jocelyn a sad look and shook her head. Though she was enslaved to Valentine and, by extension, this woman, she couldn't turn away from a mother living in fear for her son. Since the nurse didn't know Jonathan, at least not in any real way, she could sympathize with Jocelyn. "He's alive, miss."

"I know," Jocelyn sobbed, "but just look at him. He's got a fever, and he shakes, and seizes, and moans something horrible. I can't bear to watch my son like this. What's wrong with him?"

"No one knows, miss," said the nurse kindly. "Your husband brought him here, saying he had collapsed a day ago in a fit. Perhaps this is demon work? Perhaps your son was wounded in the battle by a demon and just now the poison has reached his heart?"

"That was months ago!" Jocelyn cried, and she gave Jonathan a faint shake. "Oh, Jonathan, please, wake up. Just open your eyes; don't go…"

"I do not think he will die, miss; your son is strong." The nurse went to reach for Jocelyn's shoulder, but the other woman pulled away with a dark look at the nurse.

"My son is strong? Yes, I know that, thank you, but to what end did it get him?" Jocelyn tossed her hair over her shoulder and returned her focus to her son. "Bring me my husband."

"Yes, miss," sniffed the nurse, and then left, regretting showing Jocelyn Morgenstern any pity.

"Jonathan, please wake up." Jocelyn sat with him, hoping he might mutter something to her again, and a small part of her wondered how this had happened.

_He was will, was all, _she thought. _My little boy, the son I thought dead, he was ill._

Yes, but what? hissed another voice in her head. What made him so ill?

_Jonathan has just been overworked by Valentine, busy with the Clave. I should have seen him more often, offered him my help more. When he wakes up I'll never leave his side._

You mean when you left his side as he burned alive in your parents' house?

_But he didn't die. Jonathan and Valentine returned to me, and I had a family all over again. It was me and Valentine and Jonathan and Clary…_

Clary…?

_Clary wanted a family too; she was always mooning after Luke to be her father, but why bother now that she has a real father and real brother? Clary is happy-will be happy-when this is all settled. Valentine will bring Clary back to me._

Valentine will hurt Clary, you know? You've seen him do it. You've watched while he beats her and Jace and then you leave them. What kind of mother are you?

_Clary needs to learn discipline, she needs to learn control, or else how will she become a great shadowhunter? Valentine loved you, and loves the children you bore him, he tells you every day. One day, when Clary is older and married, she will be grateful Valentine raised her as he did. Clary will love him just like you._

"Stop…"

"Jonathan?" Jocelyn asked at once, and she cupped his cheek in her palm. "Jonathan, are you awake?"

"Where am I?" Jonathan asked though his voice was weak and gravelly, like he hadn't had water in days.

"You're in Idris, Jonathan, in your room at home. Everything is alright, Jonathan, everything is going to be okay."

Jonathan opened his eyes and squinted up at Jocelyn. Her face was haggard with shadows under her eyes and worry lines in her face. She seemed to be possessed by a frantic energy, and every movement was shaking and uncertain. Jonathan had never really liked Jocelyn, not in any loving way, anyway. He knew Valentine loved her-was obsessed with her-so he had accepted her presence and her sickening motherly ministrations. Now, however, glancing up at her, Jonathan felt a strange stirring in his belly, though he couldn't name the feeling.

_Just kill her, just tear out her throat and watch the stupid bitch bleed out, _he hissed at himself. _That's what you're feeling-finally-you're feeling the urge to kill your own mother. This is just more proof that the Angel is leaving you; you're becoming a demon in full._

"Where is my father?" Jonathan asked dryly, staring at Jocelyn with huge, reflective eyes. "I need to speak with my father."

"He'll be here soon, Jonathan," Jocelyn promised. "I told him I would stay with you while you slept and recovered. You passed out almost a day ago."

Jonathan blinked in surprise. "A day?" he croaked. "That's not possible. I don't-I never…"

"Perhaps it is good for you, Jonathan," said Jocelyn gently. "You've been so busy lately, running errands for your father, consolidating power, watching Clary and Jace for me…You need to relax some."

_Just kill her. _"No."

"But you're sick, Jonathan!"

"I wasn't talking to you." Jonathan shook his head. _Where did that come from? _"I mean, I wasn't tired. Has my father found Jace and Clary yet?"

Jocelyn's face fell. "They're still gone; Valentine has been trying to track them down for a bit now-that's where he is now. I asked him, but he just said they'd ran away and are using a rune Clary made to hide from him." Jocelyn shook her head. "I do hope they come back of their own free will; it will go hard for Clary if Valentine must bring her back."

"Jace knows better," grunted Jonathan, wondering if Jocelyn knew the truth that he did.

"He's a good boy," Jocelyn agreed. "I hoped that he might prove a good influence on Clary, and I still hope he brings Clary back to me, but how they managed to hide, I'll never know."

Jonathan scowled at the mention of Jace. _She loves Angel Boy more than me. _"It's Clary, that's all. My father will bring them back soon, and after that, he'll never let them run away again. You'd like that."

Jocelyn smiled. "I just want our family to be together."

"And we will be, Jocelyn," said a voice like iron behind her. Valentine was standing in the doorway, staring at the scene before him. He had never understood the family dynamic well, and had made his own instead. Now, he speculated over what stood between Jonathan and Jocelyn. Suddenly, though, Jocelyn smiled brilliantly at Valentine, and he relaxed. So long as Jocelyn was happy, he would be pleased. "I'm going to find our wayward daughter soon."

"Don't be too hard on her, Valentine," Jocelyn said simply. "I love Clary, and even though she's a troubled young girl, there's hope. Jace has always been a good influence on our daughter. Don't punish him for her."

Valentine held out a hand to Jocelyn, who rose up and joined him, kissing him gently. "I won't. Now, why don't you go talk to the Lightwoods? I've heard they might be coming around to us."

"I would like to have Myrse to talk to again," Jocelyn said thoughtfully, and, with a last look at Jonathan, left.

"I take it, you have not found them?" Jonathan asked from the bed.

Valentine closed the door to Jonathan's bedroom with a snap and turned to face his son. His eyes raked Jonathan, seeing everything from the shallow rise and fall of his chest, to the sweat that was steaming on his skin. But that wasn't what most concerned Valentine, no, it was the look in Jonathan's eyes. There was something there, something…diminished.

"Not that I expected to," Valentine answered. "This man, this _Doctor_, I've had the Silent Brothers looking for him in the library."

"And have they found anything?" Jonathan raised one eyebrow. He hated when his father stared at him.

Valentine's lips pulled back in a snarl. "There are mentions all over, _from _all over. He keeps popping up in different places, different times, but it's always the same: right when the world is about to crumble into darkness, the _Doctor _makes an appearance."

"So, he's real?" Jonathan felt an odd flutter in his chest. _Kill the Doctor? No. _"There's really a man out there who can travel through time?"

"Impossible," snapped Valentine, but his voice held a strange note of doubt. "Whatever this Doctor man is, he's a liar. No one can travel through time. Now, how he's managed to hide Clary and Jace from me, that's something I've been mulling over."

"How do you figure that?"

Valentine passed by his stationary son and stared out the window at the city below. "He must be a warlock. Using a spell to make his home travel through the dimensions."

"Like our apartment," Jonathan mused. _No, the apartment couldn't travel through time. _"How do you account for him cropping up all through history?"

"Don't be a fool!" Valentine snapped. "Clearly, a warlock might live a long time, and that's what this man is. He's just a clever warlock, but what he wants with Clary and Jace, I don't know."

"What if he meant what he said? What if he's here to stop us?" A pang of something raced through his heart. What was it…? _Fear, you're feeling fear._

"Us?" asked Valentine sharply. "I was unaware you were still at my side, Jonathan. I thought, perhaps, this sickness might have taken you from me."

Jonathan raised an eyebrow. "Whatever do you mean, Father?"

"You are weak," Valentine said simply. "I see it in you, Jonathan. Whatever has happened to you, whatever might have caused it-and I suspect your runt of a sister-it has changed you."

"I am still your son, still fighting for your cause," Jonathan said evenly.

"That remains to be seen," shrugged Valentine. "You are certainly not ready for any action today, probably not tomorrow, and I need swift action now."

"Let me help-"

"The Lightwoods brats are gone."

"That's not possible," said Jonathan swiftly. "I saw them into their cell myself!" _Perhaps you're failing yourself?_

"Then where are they, Jonathan!" Valentine snarled, turning about to face him. "I went to question them, and what do I find? An empty cell, chains broken, and scorch marks on the wall! Who do _you_ think is behind it?"

"The Doctor-"

"The warlock, Magnus Bane, has gone missing." Valentine turned away, but Jonathan saw the hands clasped behind his back turn white at the knuckles. "We were keeping tabs on him, and today, suddenly, he was gone. I suspect Clary and Jace were behind it, probably with the help of the Lightwoods they freed."

_Jace and Clary hiding, the Lightwoods breaking free, and warlocks vanishing…how can you deny his strength? _Jonathan shuddered a little. "I'll help."

"And then there is you," Valentine growled.

"Me?"

"The Doctor threatened action, he threatened to right what was wrong, didn't he?" Valentine's eyes turned sharply on Jonathan and stared, unforgiving. "_You_, Jonathan, are certainly wrong. Not three days ago he helped Jace and Clary escape and swore to stop me, and yesterday, the Soul Sword dissolves and you collapse. You must see a connection?"

Jonathan swallowed. "The Soul Sword is a weapon of the Angel. I am not."

Valentine shrugged. "You are both weapons of mine, or, you were."

"I still am!" Jonathan snapped, and his eyes turned hard. "Give me just one more day and I'll be back on my feet. I'll help you track down the brats and kill that Doctor."

"You'll do no such thing," Valentine said softly. "There is too much at stake, and too much I don't know about the Doctor. You will remain here, Jonathan, until what you have become is revealed. I will leave Jocelyn with you."

"I don't want Jocelyn!"

"You will stay," he ordered, and Jonathan was shocked to find that he too, was bound by the runes he bore to serve his father. "I will return in a few days time to check on you, Jonathan. Behave yourself while I am gone; I haven't had to discipline you since you were a boy." He smirked, and Jonathan felt a surge of anger, but he passed by and left the room, closing the door with a snap.

_What have I become that my own father doesn't want me?_


	15. Abduction

Abduction 

_I don't know, it's a thing in progress. Respect the thing!_

_-The Doctor_

"So, you're Magnus Bane, are you?" asked the Doctor, smiling his usual boyish smile at the warlock. "I like your coat." River and Amy rolled their eyes. Of course the Doctor would like Magnus's coat; it was an old-fashioned, waist-length plum number with black trimming and details around the cuffs and collar.

"I like your bowtie," replied Magnus after a minute of long silence.

"See," the Doctor shot at River. "Bowties are cool. I'm the Doctor, and this is my Tardis. It travels through space and time," he added, smiling to himself.

"So I've heard," Magnus muttered, looking around the shaking, metal room. "I must admit, of all the ways I expected to be reunited with Alec, it certainly wasn't this. Where exactly did you find this…did you call it a Tardis?"

"Yes, my Tardis. It's an acronym; it means Time And Relative Dimensions In Space." The Doctor rocked back and forth on his heels and then glanced over at River who was repressing a smile.

"Yes, but where did you get it?" asked Magnus.

"Ah, well, yes," said the Doctor, fiddling with his bowtie. "I'm a Timelord from another planet. My friends and I were minding our own business, floating about in space when we passed by a white hole. It overpowered the Tardis's circuitry and we were in a bit of free fall. Ended up in New York City. It was very fun."

Magnus raised his eyebrows. "Fun? Yes, that certainly sounds like it. So, I'm wondering, what exactly have you done? About four hours ago, I was sitting in the basement of a brownstone in New York City, trying to find anything that might help me free the Lightwoods from Valentine when I felt a very powerful tug. I went outside, looked up into the skies, and what should I see? The very heavens exploding with light as every demon in the world was torn apart. Why is that?"

"That was Clary," answered the Doctor, and beckoned her forward.

Clary drew up and smiled shyly at Magnus. "I made a rune, one that could draw all the demons to us, and then the Doctor did this thing, and he sent them all into a hole in space."

"How did you draw the rune?"

"We used the Tardis and moved stars to draw it in the sky." Clary blushed. "The Doctor did most of it; I just came up with the rune!"

Magnus glanced from Clary to the Doctor and then over to Alec, who was seated behind him, looking tired and worn, but pleased. "You said the Doctor did a thing?"

"Respect the thing," the Doctor said swiftly and Amy's smile widened.

Again, Magnus fell silent as he mulled over what he heard. "And you say you're going to Idris now and Jace and Clary are going to lure Valentine into the Tardis because of the temporal-temporal-"

"Temporal Grace Unit," supplied River, "which, I might add, I fixed-_alone_."

"Yes, right," waved Magnus. "Because if Valentine is in the Tardis, he'll be rendered helpless. So long as he's in here, we'll have all the time in the world to free the shadowhunters from his power."

"I've been thinking, Doctor," said Jace, stirring from his place and upsetting Max, who had been sleeping on his lap. "Do you think Clary might be able to design another rune, and you'd be able to use the Tardis again to amplify it? It would take days for Clary to mark every shadowhunter…"

"It would be difficult," the Doctor muttered. "Besides, if I use the Tardis, the radiation might actually do damage to the shadowhunters."

"What about the Mortal Instruments?" piped up Isabelle. "Valentine used them to do this to us in the first place, what if we use the Mortal Cup and-"

"It's been destroyed," the Doctor said softly.

"_What_?" Isabelle, Alec, Jace, Clary, and Magnus all said at once.

The Doctor looked about nervously. "Well, Valentine turned the Mortal Instruments to demonic power, so, when Clary drew the rune, it drew all demonic things to it-including the Instruments. They were probably atomized."

"Can they be remade?" asked Jace, wondering what _atomized _meant.

"Maybe," the Doctor mused. "It's possible. I suppose if we got the pieces together we might be able to reform them, and then Clary could mark them with some runes. We could summon the angel again, have him polarize the cup, and any shadowhunter who drinks from it should experience a magnetizing effect, reversing the hormone cascade-"

"What are you talking about?" Isabelle said loudly, cutting the Doctor off.

The Doctor smiled guiltily. "Sorry, got a little ahead of myself, what I mean to say is that if we summon the angel again, he could reverse the effects of the cup, and anyone who drinks from it will be freed from Valentine."

"Where are the pieces?" Jace asked.

"Well, we can assume that Valentine wouldn't have just gotten rid of something so valuable," Clary mused. "They're probably right where they were the moment they dissolved."

Jace and Alec looked up nervously to each other. "You mean in Idris?"

"I would guess," Clary said. "We'll have to go to Idris, sneak into his home, and then gather what's left of it. Is it safe to land the Tardis in Idris now that Valentine knows we can travel there?"

"Only one way to find out," said the Doctor with glowing eyes. "Let's locate the cup on the Tardis sensors. Everyone, hold on for a bumpy ride." He seemed ridiculously overjoyed by that fact, and bounced all the way to controls.

Clary and Jace slunk away to a corner by the stairs and Clary nodded upwards. "Do you think there's time for a nap? I'm dead on my feet and I don't know why…"

Jace smiled sympathetically. "It's been over a day since we last slept, Clary. Things just get a little busy here, I guess."

"Go nap," said Amy, sneaking around the stairs and smiling in a way that reminded Clary of her mother. "Time gets complicated when you live on the Tardis, you forget when you ate, when you slept, when you were last on a proper planet. Just try to get used to it for now. You'll get accustomed."

As Jace and Clary settled down for a nap, Alec drew Magnus aside and offered him a bit a food from the dinner they'd had. Magnus took is greedily and began eating as fast as he could. "Have you been in hiding this whole time?" Alec asked.

Magnus swallowed. "Well, I didn't have much of a choice, did I? After the war, everything went to hell; hundreds of Downworlders were slaughtered by the demons Valentine had summoned, and the ones who didn't made for the woods. I went with them."

Alec was dying to know how Magnus was, and, more importantly, how he felt towards him. "What made you go to New York? You must have had so many other places…"

"Well," Magnus said contemplatively, "I know the city well, and I have many safe places there, enchantments I'd made, traps I'd set. I knew I could hide there for at least a year before having to move. Also, I suspected your parents and Lucian might be trying to lead some rebellion, and they would be in New York." He paused a moment, seeing Alec's glowing eyes. "And, I'd heard you and your siblings had been moved back to the Institute, and I wanted to see if there was any way I might be able to set you free."

Alec shuddered. "We were being watched too closely, and besides, if you would have given up hiding, Jonathan would have killed you. He split his time between New York and Idris, and he was at the Institute with us, trying to train us."

"Train you?"

"Well, Valentine said we were still part of the Clave, regardless of what our parents were, and he was going to see us properly trained. I have to admit, I understand why Jace is such a good fighter." Alec rubber his shoulder, still sore from a few days before when Jonathan had hit him with the flat of a sword. "Valentine said he would train the new generation like he had Jace and Jonathan, and we were going to be the first children to have that honor. I'm glad we got Max away before they hurt him."

Magnus glanced over at Max, who was sitting with Isabelle, his eyes unable to stay in one place. "How did you escape?"

Alec smiled ruefully. "Valentine thought we knew something about Jace and Clary's escape, so he dragged us off to Idris. I think he planned to use us to draw them in, like bait. But the Doctor flew the-the Tardis into Idris and landed right in our cell. We climbed on and were gone." Alec looked around the room again. "I don't know how he did it, I don't even understand him half the time, but the Doctor managed to fly that thing right in."

Magnus studied the room. "I've never seen a place like this before; where did this man come from?"

Alec lowered his voice. "He's from another planet. Jace said Gali-Galifrey, or something like that."

"An alien," mused Magnus. "Well, why not? We've got angels and demons, why not Martians? And his friends?"

"Well, the woman with red hair is Amy and that's her husband, Rory. I'm not sure this makes sense, but the other woman, with the curly hair, is the Doctor's wife, who is Amy and Rory's daughter." Alec gave River a long, considering look. "Can't say I understand it."

"When you travel through time you're bound to have fumbles," was all Magnus said, and then turned to see the Doctor clapping his hands and spinning around to face them. "An announcement?"

"Right-o, Magnus," said the Doctor, and then frowned more to himself. "I'm not saying _that _again. Anyway, I've locked the Tardis onto the Mortal Cup's signal. I'll be able to follow it back to Idris and through any of the protective spells Valentine has put up around it."

"If he's left someone to protect it-" Isabelle said uncertainly.

"We can handle that," said River with a gleaming smile. "I mean, what're we up against, Jonathan?" She laughed as though the prospect of the most dangerous shadowhunter were nothing to her.

The Doctor, though, seemed deep in thought. "Whatever we find, we'll be able to maneuver around it, especially if we get it in the Tardis. Where are Jace and Clary?"

"Went for a nap," shrugged Amy.

"Well, wake them up!" the Doctor cried outraged. "Here I am, being brilliant, about to save their entire civilization, and they're asleep? Honestly, what do I keep you lot around for anyway?"

Amy rolled her eyes and went to find the sleeping beauties. Behind her, Rory rolled back and forth on the balls of his feet. "So, do we need to get ready for battle or something…?"

"Well, it's not exactly a war, is it, Rory?" mocked the Doctor. "No, I think if we just land the Tardis and sneak out we should be able to grab the cup and run for it."

"You do an awful lot of running," observed Isabelle.

"Yes," agreed the Doctor, and he as very happy to hear it. "Amy! Where are Jace and Clary?"

"What am I, your bellhop?" Amy demanded, coming down the stairs with a sleep ridden Jace and Clary in tow. "Amy, do this, Amy, do that, Amy, fix everything!"

"I never ask you to fix things," laughed the Doctor. "Jace, Clary, we're approaching Idris and the Cup. Thought it might be a good idea to have your two ready for it."

Jace blinked. "We're _back_?" he asked, feeling that he was never going to get used to the constant jumping around. "I thought we just _left._"

"Yeah, well, we had to get the Lightwoods and then go find Magnus, and there was the whole moving the stars things. We had _stuff _to do," the Doctor said, making wide hand gestures. "But, yes, now we're going back. Fancy a family visit?"

"No," said Jace swiftly, hoping he wouldn't have to run into Valentine or Jonathan until it this was all over. "I don't think Valentine is going to be expecting this either. He was always a man of action, and he would be planning for me to strike with some sort of weapon."

"That's where the timelords differ," shrugged the Doctor. "We're not much as fighters go, but we're _very _smart."

Jace smiled in return and went to join Alec and Magnus while the Doctor drew River aside and they began punching buttons on the controls. The Tardis gave a shudder and Jace and Clary braced themselves, already growing used to the feeling of the shaky, bumpy ride that awaited them. Clary smiled recklessly up at Jace.

"I could like this, Jace," she whispered softly, eyeing the Doctor from her seat. "I could like traveling like this very much."

* * *

_This is painful, _Jonathan thought, trapped in his bed, listening to his mother talk to him about nothing. _She doesn't shut up, she doesn't say anything, she doesn't matter. By the Angel, why don't I just kill her?_ Jonathan eyed his mother speculatively, his fingers twitching, longing for a weapon of some sort. _I could do it, it wouldn't be too hard, all I need is a nice, serrated knife. _

_Then why haven't you done anything about it? _asked a small voice in the back of his mind. _If you want her dead so much, put your money where your mouth is._

The fact remained that Jonathan felt himself flinch away from the idea of killing his mother. It had started as nothing so much as a twinge in his stomach, like his belly was doing nervous flips, but, Jonathan had reasoned, he didn't get nervous. Instead, he had fought back, thinking darker, more terrible thoughts, but the twinge grew into an unpleasant lingering in his chest. His plans to kill his own mother were being constantly met with an argument with his conscious, and it was wearing his patients thin. Why was he losing his nerve?

_You're sick, that's all, _he tried to convince himself. _It's the Angel blood fighting back, trying to punish you for what you're becoming. You'll just have to wait it out, but, god, if you listen to this woman any longer, you'll be dead before you're free._

"…father was always so charismatic; you two share that quality, you know. Men and women were happy to follow Valentine, and, they're enamored with you. I'm sure when your father and I are gone, you'll prove an excellent leader of the Clave." Jonathan groaned, but Jocelyn mistook it for pain. "Are you alright, Jonathan, would you like some water or more soup?"

"I'm fine, Mother," Jonathan ground out, casting her an unfriendly look. "When will my father be back? He's been gone more than a day."

"Oh, Jonathan," said Jocelyn, and she cupped his face in her hands. "You don't need to worry about him. He still loves you, he still wants you; Valentine is just worried you're ill and he doesn't want to strain you."

"Strain me?" he asked, incredulous. "I'm not strained, Mother. I want to help Father fight this Doctor and get my sister back."

"And Jace," said Jocelyn blankly.

"And Jace," Jonathan agreed bitterly. "They could be in danger, or, planning some of that rebellion nonsense. You know that has to be put to an end."

Jocelyn looked away. "I know Clary has a rebellious streak in her, but she's just acting out. I think she feels a little shafted since your father and I reconciled; she doesn't know quite where she fits in a family with a father, mother and brother. I had hoped having Jace around would help her transition better, but she was just a bad influence…"

"Maybe," mused Jonathan, disguising some of the hope in his voice, "you can send Jace away? Not for long, of course, just long enough to teach her a lesson. I don't know how well she responds to Father's ministrations."

"Well, perhaps," Jocelyn sighed, "but I think Jace can still prove to be a useful influence on her. No doubt, though, she has been foolish. Clary is going to have to be punished."

_She deserves it,_ hissed a voice in Jonathan's head, to which another said, _Does she really? _Disconcerted by the argument in his mind, Jonathan stretched and tested his limbs. "Father told me the Mortal Instruments were gone; has he disposed of what remained?"

Jocelyn smiled a little helplessly. "I do believe he kept most of the pieces, though why, I'll never know. Perhaps he hopes to remake them some day? I'm a little worried, of course, as to what could have damaged the craft of the Angel?"

_A demon?_ snickered the voice in Jonathan's head. "It is certainly disturbing that this Doctor fellow could do such damage without even being in the city. But, I'm certain Father will find him and dispose of him."

Jocelyn looked displeased. "Sometimes, I wish your father wouldn't be so concerned with the greater good of society and the world, and I wish he'd just stay at home with us. You had all childhood growing up with him, but Clary…" Jocelyn gave herself a shake. "Listen to me, warbling about things like family. You probably want something to do; a book, maybe?"

Jonathan wanted to scream and shake the life out of his mother, but he forced his face into that charming smile he saved for her. "Actually, I'd like to take a walk; see how the city fares without its great protector. Also, I'm a little curious to see what has become of the Mortal Instruments. Do you know where he's keeping them?"

"Off the library in his private study," Jocelyn said aimlessly. "Don't get too obsessed with them, Jonathan. It's not as though the world is going to end without them."

"I wouldn't be so sure, Mother," grunted Jonathan, and he swung his legs around and tested his weight on them. At first, he pitched forward, and Jocelyn rushed forward to meet him, offering him her arms as support. Jonathan felt the usually anger surge up, but it was fought down by something else, though he couldn't name it. "It's alright, Mother, I can walk myself."

"Be careful," she pleaded, and then watched while Jonathan gained better control over his legs and struggled to the door. "I'll come for you shortly when dinner is ready."

Jonathan barely registered what she had said as he fled the room and his mother's emotions. Slowly, with much concentration on his steps, Jonathan made his way to the library in their house, and then to the private study where Valentine would spend hours. Jonathan had never really liked the study, personally, since it reminded him forcefully of his childhood. He still had memories of Valentine's overbearing presence in his childhood, all of them dark and even disturbing. He scrunched his nose as he surveyed the room.

_So, where are the Instruments? _Jonathan wondered, padding around the desk. He saw maps of Idris and the surrounding countries, records of weapon production, and ledgers and ledgers of names. Jonathan flipped through a few sheets aimlessly, and came upon a single piece of parchment, with the name _Doctor_ written on it but nothing else; Jonathan smiled without humor. _Just dust, that's all that's left. _Jonathan ducked under the desk for the lower drawers when he heard faint voices echoing toward him. He narrowed his eyes, waiting to see who was creeping about their house, and cursed his father for taking away his weapons.

When the door creaked, Jonathan launched himself over the desk, but skidded to a halt. "_Jace_."

Jace was taken aback and reached to his belt for a weapon, but didn't find one. "Jonathan," he returned icily. There was movement behind him, and Jace made a frantic step back, calling out: "No, Clary, don't-"

But too late. Clary came around the corner as well and started when she saw her brother there. "I should have known Valentine would leave you here to wait for us." Her eyes flashed angrily and Jonathan wanted to give her a good shake.

"No quite, little sister," Jonathan growled.

"What's the hold up!" cried a voice from the hall, and a woman came around the corner, tossing back a lot of red hair. "I thought we were on a mission? You know, sneak in, sneak out, grab the Mortal Instruments on the way."

"You?" demanded Jonathan, eyeing the woman. He recognized the red haired woman as if from another life. It seemed years ago that he had met Amy Pond outside the school with Jace and Clary. "What are you doing here?"

"Fancy seeing you, Jonathan," Amy said, unimpressed. "Do you mind telling us where your father put the Mortal Instruments?"

"She's a Mundane," Jonathan shot at Jace and Clary. "If you thought you were in trouble now, Father is going to kill you. You can't just parade Mundanes around Idris."

"This isn't a parade," said another voice, and Jonathan saw Mr. Smith stroll in. "It's a traffic jam, clearly. Why have we stopped?" Mr. Smith saw Jonathan and, he alone, smiled easily. "Ah, that's the ticket."

"Mr. Smith?" asked Jonathan. "Or, do you prefer to go by the Doctor?"

"Please, call me the Doctor, it's easier to remember," he shrugged. "Oy, Rory, we found the Instruments, get in here!"

Rory came in, glanced around and saw Jonathan. "How can you tell?"

"Well, why else would Jonathan be in here if not to guard them?" asked the Doctor quickly. "I do hope the Lightwoods found their. Mind telling us where you're keeping him?" he shot at Jonathan, who glowered. "Or, not."

"So, here to get the Instruments?" he asked Clary. "You two are in trouble, you know. Father is very displeased with your recent display. If I were you, I'd just give up now and see if you can't get a little mercy."

Clary shuddered, but she determined not to show her fear to Jonathan. Not anymore. "We're here to stop him, Jonathan, and it's you who should be asking for mercy."

Jonathan smirked but turned to Jace. "She's got a mouth on her; I thought we'd almost fix that? I guess when you give her a little freedom it goes to her head."

"Shut up," said Jace softly. "And stand aside. We know that the demons are gone, Jonathan, and that Valentine's power is failing without them."

Jonathan bared his teeth. Jealously and anger still burned for Jace, and he longed for a knife to run through him. "You have no idea what he's capable of."

"You don't know what we can do," said the Doctor, sensing the tension between the two brothers. "Jonathan, I'd like to help you if you'll let me, but you're going to have to step aside and give us the Instruments."

"I don't think so," Jonathan smiled grimly. "I don't want or need your help, Doctor."

"Too bad, cause you're going to get it," he replied, and Jace heard that steely note in his voice again. "Now, step aside; we don't want to hurt you."

"I want to hurt you," said Jonathan politely, and then lunged at them.

At that moment, though, River Song appeared. She spotted Jonathan just as he dove, and fired at him in midair. River's aim was true, and she hit Jonathan square in the chest. It was only a stun gun, and so Jonathan fell out of the air, landing in a heap of limbs on the floor. Jace stared at Jonathan and then turned to face River.

"Where were you eight months ago when I needed to kill him?"

River smiled like a razor. "Eight months ago? Saving a planet. Now, go on, get! Grab the Instruments and let's go."

The Doctor went to inspect Jonathan while Clary, Jace, Rory, and Amy tore the room apart. After a moment, River joined him. "What do you make of the boy, Doctor?"

"I think we should take him with us," the Doctor finally said. "I think I can help him if I can just get him away from his father's influence and calm him down."

"But on the Tardis?"

The Doctor shrugged. "Whose he gonna hurt?"

River looked uncertain, but she knew she was in no position to argue. After all, she _had _been tried for murdering the Doctor. "Alright, alright, we can probably keep him in the library, or the pool room, or the green house, or-"

"Or a bedroom," said the Doctor firmly. "He's very ill, River, not an animal. We can program the door to lock so he won't go after Jace or Clary, and we can try and drain the poison."

River still seemed perturbed, but the Doctor carefully scooped Jonathan up. It was lucky he was taller than the boy or it would have made their escape rather ungainly. When Jace and Clary looked over to the Doctor, their mouths dropped open. "You can't," they both said.

The Doctor's eyes turned steely. "Have you found the Instruments?"

"You can't bring him!" Clary cried, coming around the table. "He tried to kill Jace, and he hates me, and he'll try and kill you for my father."

"Clary, this isn't up for debate. Now, find the Instruments and go back to the Tardis." The Doctor's voice put an end to any argument, and Clary still didn't have enough nerve to challenge him.

"You can't help him, Doctor," she said weakly.

"It's what I do," said the Doctor simply, and shifted Jonathan's weight so he could carry him better.


	16. Mercy

**Hello everyone! If any of you follow this story, you might have seen an update, but then it was gone. That was my fault! I posted a chapter here that belonged to another story I'm working on. Anyway, a few different people let me know, so, thank you! Also, since this story is winding down, I have begun work on another, independent Mortal Instruments fanfic. It's nothing to do with anything else I have written, and is not a crossover, but if any of you have enjoyed my writing style, I will have something new posted soon.**

Mercy

_We all carry our prisons with us. Mine is my past, yours is your morality._

_-Kahler-Jex_

Jonathan stirred in his sleep, feeling that he had been rendered unconscious too many times these last few days. Carefully, Jonathan stretched his toes and fingers, feeling for anything that might give him a clue to where he was. His last memories were of his attack on Jace, Clary and the Doctor, and the fleeting glimpse of a strange woman firing a gun at him. He wondered if he hadn't been imprisoned and was waiting for his execution; surely, whatever rebels Jace and Clary had amassed would want him dead? This also raised the question of what might this alien Doctor want to do with him. Beneath his fingers, Jonathan felt only starched fabric and the soft, giving cushion of a mattress.

_So, where has sweet little sister locked me up? _Jonathan asked himself, and then slowly, very slowly, opened his eyes.

Jonathan didn't know what to make of the room he was in. It seemed to be a sort of bedroom, at least the bed he was lying in, the dresser full of drawers, and the closet suggested it. The walls, however, were made of copper colored metal, with a number of bulging, metal bulbs, and they stretched up into the darkness. Jonathan supposed that somewhere above him, there must be a ceiling, but he couldn't see it, even when he strained his eyes. Every now and then, the room shook a little, but Jonathan and the bed remained firmly attached to the floor. Across from his bed was a plain looking door.

"Clarissa," Jonathan growled, thinking she must be watching him, waiting for him to wake up and try and break free. "Jace. I know you're here somewhere." Jonathan hung back a moment, and then, as if to shock them, launched himself from the bed and at the door. The door didn't give, so he shook the handle, pounding on it. It still didn't want to move. "Is this a game to you; locking me and up and making me wait just like Valentine did to you?"

_That'll be it, _Jonathan though contemplatively. _They want their revenge, is all. They'll leave me in here a while, letting me stew, watching me die; then, when I'm on my last breath, I suppose they'll make their appearance._

Jonathan backed away from the door and sat carefully on his bed, looking like nothing to much as a diligent young man. He turned his thoughts on the Doctor, the alien behind the escape. His last fleeting glimpse had been of a young man, dark haired and dark eyed, with a very serious face for one so young. Though he had been open and seemed rather pleased with their break-in, Jonathan had sensed a darkness in the man. So, had this Doctor made plans for him, the demon son of Valentine? The Doctor had said he was going to fix what wrongs Valentine had wrought, so did that mean he was going to _fix _him?

_Killing me is more than likely the best way to remove me from the picture,_ Jonathan reasoned. At first, it didn't really bother him, his upcoming demise, but as Jonathan sat there, going over and over his fate that small, creeping voice whispered in his mind, _I don't want to die, I don't want to die. I have a life to live, people to meet, places I should see. It can't end here._

Jonathan gave himself a shake. "Let them come, let them kill me. Whether in this life or the next, I'm for the darkness."

"You think that, do you?"

Jonathan jerked up, his dark eyes pinioning on the tall figure, standing in the shadows of the door. He watched as the tall Doctor emerged, his face calm and grave and his eyes staring down at the ground. Jonathan felt the urge to throttle the life out this man, but he got the feeling that Doctor was much more than he seemed, and underestimating him might not prove too well.

"Sorry, didn't catch that, Doctor." Jonathan smirked but remained seated.

"Do you really think you're so lost Jonathan?" the Doctor asked, lifting his eyes and holding Jonathan's dark gaze. "Do you think life and death are so meaningless?"

Jonathan's eyes narrowed but his smile stayed fixed in its place. "Well, for one such as me, they are. I can safely assume you know a great deal about my past?" The Doctor nodded. "Then you know what I am, what I'm made of. My death will be much the same as my life, and I was never very impressed with life." _Liar, _hissed the voice in his mind.

"Perhaps you've just been living the wrong way?" offered the Doctor, drawing nearer to the boy. "This universe is a wonderful place, you know, full of amazing things you could only just imagine."

"I'm sure," sniffed Jonathan. "But I'm not really interested in this universe. I'm not sure if anyone let you in on the secret, Doctor, but there are more worlds, more universes."

The Doctor couldn't help the smile that slid over his face. "Jonathan, I'm older than I look, and not what I seem. I have walked in those universes, seen what lies beyond this place. I'll tell you something, Jonathan, it's all the same. It's all endless dark sky filled with flaming balls of gas, and all the while, insignificant life forms make their way day by day, year by year."

"Then I would have them as mine," answered Jonathan, uncertain if the Doctor was speaking the truth.

"You don't want to take over the universe," he said sadly. "You wouldn't know what to do beside shout at it. There's a lot of nothing up there, Jonathan."

Jonathan frowned. "And you have the alternative, do you?"

"I could help you, Jonathan," the Doctor said, and in his eyes was that light again; the light of a passionate, caring man. "I could make you better, Jonathan; drain the poison out and give you the life you deserve."

_Freedom?_ he thought hopefully, but crushed it quickly. "This is the life I deserve."

"That's not true," urged the Doctor. "You're not some evil monster, Jonathan, you're a boy who has a horrible past. What your father and Lilith did to you wasn't you fault, and it was wrong. You're meant for more than this-this darkness and loneliness."

"And what would you know of it?" spat Jonathan. "You, who travels the universe, righting wrongs and saving lives; wearing that stupid smile and thinking you can make darkness into light. What do you know of anything?"

"I knew a man once," said the Doctor swiftly, and he seemed to Jonathan, immeasurably sad. "A man like me, a Timelord called the Master. He was just like you, Jonathan; his childhood had been poisoned by someone he trusted, and it drove him mad. He was consumed with this madness and trapped by his own anger, and there was no one there he could take it out on-because of me."

"Why only you?" asked Jonathan, giving him a once over. "What did you do?"

"Do you know why I'm called the Destroyer of Worlds?" When Jonathan stared blankly back, the Doctor ran a hand through his hair. "I destroyed a planet and everyone on it; we were at war, and it changed my people, and I didn't have a choice, but I still did it. And how could the Master punish the man who hurt him when I'd killed him? So, he only had me."

Jonathan laughed. "How'd that work out for you?"

"Well, in the end, after he'd fought and tortured and ruined countless lives, he saved the universe." The Doctor shrugged. "Funny, how these things happen, really."

"Not much of a story, if you ask me," Jonathan dismissed. "And I hardly see what it has to do with me."

"He wanted to be master of this universe, but he realized in the end what that would have meant, how lonely that would have been," the Doctor said, and Jonathan realized that the Doctor was now standing a few feet away. "The Master wasn't inherently evil, and neither are you, Jonathan."

"You can't say that for sure," Jonathan said, staring down at his hands. "I have had demon blood in me since before I was born. I am evil."

"That was done to you," the Doctor said firmly. "It wasn't your choice, and if you had the chance, I don't think you would choose it this was. Naturally, of course, I will not be punishing you for something beyond your control."

Jonathan's eyes widened at the statement, and though he was still looking down at his hands, he felt his heart quicken. _How can he _not_ punish you after everything you have done? Everyone wants you dead, everyone but Lilith; you're their greatest fear, their deepest hatred, the darkness they run from…He must be lying._

"You'll forgive me, Doctor, but I find that hard to believe." Jonathan composed his face and then leveled the Doctor with a sardonic smile. "Surely my sweet little sister and her lover, Jace have been telling you all about the horrible things I did? And, you have the Lightwoods with you, I hear? They, too, are not fond of me. What have they told you?"

"Whatever they have said, I'm not so foolish to take it at face value," the Doctor replied subversively. "I think, after a thousand years, I know enough about how this universe and the people in it work, to know when I'm looking at a person in need."

"I'm not in need," Jonathan growled.

"I beg to differ." The Doctor finally sank down on the bed beside Jonathan and smiled at him. "For all your darkness, I know what you are, and that's a young man who's ill and needs help."

_He's lying_…hissed the voice in his head, but another answered, _He wants to help, he wants to give you the life you should have had. _"You'll understand that I don't see you as the man who had any knowledge of the darkness I was born with. You travel the universe, saving lives because it appeases some desire to do good; my desire is to see it all turned to ash."

"You're wrong, you know," said the Doctor in an odd voice, "about me, I mean. I don't travel the universe to do good because of a desire to see light conquer dark. If you really want to know, I've very little interest in good and evil, light and dark. As a child, Timelords learn that most of what happens can be changed, altered, made better _or_ worse, and so, it's completely unimportant. If something can be changed because you don't like how it looks, just go ahead and change it. But-_but_!-there are some things that can't be changed, events that _have _to happen. Set points in time. If these things fail to go as planned, the entire universe can end up bursting into a ball of flame. So, you see, don't you, why I don't believe in evil and good?"

Jonathan stared at the Doctor and felt his stomach doing little flips like a trapeze swinger. Did this man really not care for all the bad things he had done. "I don't understand," he admitted.

"There are only two types of events in this universe: set and variable. The variable ones, I can change; the set ones, they have to happen. Either I can change the course of history or I can't." He shrugged like it were obvious and quaint. "This makes my choices about you very simple. Either your life is variable, in which case, I can fix it; or, your life is set, in which case, you were truly _meant _to be this way, and if you're not, the universe falls apart. So it is rather heartening, isn't it? If you really are meant to be like this, the entire universe depends _on_ you being like this."

Slowly, Jonathan blinked, trying and grasp what the Doctor had just said. "So you don't think after all the lives I've taken I'm wrong?"

"No, you were most certainly wrong to take those lives," the Doctor said thoughtfully, "but was it really your choice? Now that is a different matter."

"I've killed hundreds of men and women, and I'll keep doing it if you let me," warned Jonathan, though a part of him took great pleasure in the thought.

The Doctor laughed, but there was no humor in it. "Hundreds? I've killed _millions_. I was responsible for the extinction of the oldest, wisest, most powerful race in the history of the universe. You want to turn this planet to ash? I sent a planet outside of this universe." The Doctor's eyes were dark with the past, and his face was drawn in hard lines. "There is a reason I earned the name the Oncoming Storm."

Jonathan swallowed. "What race?"

When the Doctor looked up at him, he saw more pain and more anger than he had ever seen in the eyes of any other being ever. "The Timelords," he said grimly.

"But you're-"

"Why do you think I travel this universe doing good deeds; righting wrongs, as you say?" The Doctor held up a hand to silence Jonathan. "I have nowhere else to go, Jonathan. My home, my family, my friends, my people, I destroyed them all. The very planet I called home-Gallifrey-it's gone because of me. I travel because I have nowhere to land, and I fix things because it's the least I can do, and I've got all the time in the universe to fill. Let me tell you something, Jonathan, a bit of advice: you don't want to burn it all down. In the end there's nothing but dust and dark and desperate loneliness."

Jonathan glanced away, unable to hold the man's gaze a moment longer. "It is in my nature to want this world gone."

"Is it?" asked the Doctor sharply. "Tell me, Jonathan, how have you been feeling lately? Sick, maybe? And sudden changes of heart?"

"What do you know?" Jonathan growled, thinking of his father's face as he turned away from him and left him for nothing. "What have you done?"

"Nothing personally, though I helped your sister quite a lot."

"Figures she'd be involved," Jonathan spat. "What did dear, little Clarissa do?"

"An impressive summoning rune," the Doctor answered, smiling broadly at Jonathan's look of confusion. "I amplified it, of course, and we tore the demons from every corner of this universe. You might have notice that the Mortal Instruments turned to dust? Well, being demonic in origin, they were reduced to their original materials, which we collected."

"You summoned the demons where?" Jonathan asked sharply.

"A tear in the universe," the Doctor shrugged nonchalantly. "They've been destroyed, atomized, they cease to exist. Lilith included, I might add."

Jonathan's face snapped up at that. "That's not possible. She was the mother of all demons, the first of my kind. If she's gone how can I still be here?"

"Well, that would speak to your nature, wouldn't it?" hummed the Doctor, pleased with the direction of the conversation. "All things demonic were destroyed, and yet, here you are, seemingly unharmed. What do you think that means, Jonathan?"

_Impossible…_ "It means that I'm the only demon thing left in their universe."

"Why?" demanded the Doctor, jumping up and pacing as though frustrated. "Why do you humans have this stubborn will not to change? It doesn't mean you're the only demon left, it means that anything demon in you is gone! The influence Lilith had over you was torn out and sucked into that tear in space along with everything else. You're not a demon, Jonathan, you're just another normal shadowhunter boy."

_No, that's not possible; you felt it, you felt the pain in your chest. _"I'm more demon than you know."

"I think I'm smarter than you know," the Doctor responded, his eyes glimmering victoriously. "And, I think you're more stubborn than you know. Tell me, have you been feeling different lately?"

_You felt such anger…and such revulsion to yourself. _"I don't know what you're talking about."

"Yes, you do," said the Doctor. "I know you do. Which feeling was it? Fear? Love? Shame? You felt them in you, and I'm sure it scared you, but that's what it was."

_It can be possible. I was born a demon, and there's nothing my sister or this man can do about it. _"No, all I felt was pain."

"_Precisely_," said the Doctor, releasing a breath. "You were feeling pain when Clary tore the demon out of you. It must have felt like you were being torn apart; probably very painful. And what happened after the pain?"

Jonathan pressed his lips together. "I couldn't kill my mother."

"Well _that's _good," the Doctor whistled.

"I _mean_, I wanted to, but I couldn't bring myself to it," Jonathan growled. "I didn't understand it then, but…"

"But now it makes sense, doesn't it?" The Doctor was watching him carefully, waiting for Jonathan to accept what he had said. "You're not a demon, Jonathan, you're not even demonic in nature."

"Why am I here than?" Jonathan said, looking around the room, his eyes finally coming to stop on the locked door. "If I'm not dangerous, why would you lock me in this room?"

"Well, let's just say a few of the shadowhunters were concerned with how you might take to your freedom, after all, you did kinda try to kill a few of them." When Jonathan stared back, nonplussed, the Doctor continued. "We wanted to make sure you really were cured, and I offered to run a few tests before we let you out. It was strictly precautionary measures."

"I didn't know I merited my own room."

The Doctor waved him off. "You can merit as many rooms as you want; the Tardis is infinitely large on the inside."

"Are you going to let me leave?" Jonathan asked, eyeing the door again.

"After I draw a bit of your blood to test it," shrugged the Doctor. "It shouldn't really take that long. I just need to run it through the Tardis, so, may I…have a bit of blood?"

Jonathan stared at the Doctor long and hard trying to discern some betrayal or intention of harm, but the man's face was open and kind. "How much do you need?"

"Just a drop," said the Doctor and he held up a strange metal device. When Jonathan gaped at it, the Doctor winked. "It's a screwdriver."

"Not one I've ever seen."

"A _sonic _screwdriver," the Doctor amended. "All I need to do is prick your finger and run off to the console. You'll be out of here in ten minutes."

"Are you really going to let me leave?" Jonathan said at once. "Will Jace and Clary and those Lightwoods let you?"

"It's my Tardis," the Doctor said simply. "Besides, let me tell you a little about something I call a Temporal Grace Unit…"

* * *

"Valentine!"

Jocelyn rushed across the library and into Valentine's arms. She threw herself at him and the force of which they connected nearly knocked them both over. Valentine carefully wrapped his arms around her and pet her hair down. She drew a shuddering breath and looked up into his eyes with her own tearing ones.

"What happened, Jocelyn, what's wrong?" he asked gently.

"Jonathan is gone!" she gasped.

"What do you mean he's gone?" Valentine asked sharply, his eyes narrowing.

"He went to your study, to look over the Instruments and that was right before dinner." Jocelyn began walking to a seat and then collapsed. She covered her face in her hands, drawing deep breaths. "When he was ten minutes late, I went to check on him. Your study was a mess, like some sort of struggle had happened, and I thought he had been attacked. There was no blood, but the room was completely ransacked."

"Someone went through the room?" Valentine hissed.

Jocelyn didn't seem to understand his concern. "But Jonathan wasn't there! I couldn't find him, and then I searched the rest of the house, and he wasn't there either. I don't know where he's gone. You don't think…" she drew a shuddering breath. "You don't think Clary and Jace had anything to do with it?"

Valentine's eyes had darkened and he frowned. "Something to do with it? I think they had _everything_ to do with it. They're the only ones who could have overpowered Jonathan-with the help of their Doctor friend-and they're the only ones who had a reason to."

"Why are they doing this?" Jocelyn cried, as if she were truly confused about why anyone would want to hurt them. "We have only ever been good to Jace and Clary; I knew Clary had behavior issues, but this it too much. I-I wish I let you raise Clary; she would never have done something so horrible to this family if she weren't so reckless!"

Valentine smirked at Jocelyn's anger at her daughter. For so long, he had been trying to keep secret his treatment of Clary, but now that Jocelyn didn't care, he could certainly do as he liked. "Don't fear, Jocelyn, I will bring back our children, and I won't let Clary continue like this."

Jocelyn looked down, her face paling. "I don't want you to hurt her, Valentine, but I can't believe Clary could be so careless and so cruel to her own family."

"I won't hurt her," Valentine said, though he was already planning the many different ways he could punish Clary and Jace for their little display. "Jocelyn go lie down, I'll be with you in a moment. I'm just going to check over the study for any signs that could help me find them."

Though Jocelyn looked ready to argue, she caught Valentine's eye and stood up stiffly and left. As soon as she was gone, Valentine entered the study as if it were foreign territory. The place indeed looked as though it had been the sight of a fight: papers strewn everywhere, chairs upturned, books misplaced, and the many files on his desk upset. He explored the room, his eyes darting off the wall and the desk and the floor.

_Did they find the Instruments? _Valentine asked himself. _What could they want with them, even if they did? _

He knelt before his desk and pulled up the loose floorboard where he had hidden the dust that composed the Instruments. He wasn't shocked when he found the dust missing; he knew they had come for the Instruments not Jonathan. After a cursory search of the rest of the room, he kicked the upturned chair in his anger.

_This isn't over, Clarissa, not even close._ He stormed out of the study, not even the least bit concerned about Jonathan.


	17. The Horrible Truth

The Horrible Truth 

_The universe has to move forward. Pain and loss, they define us as much as happiness and love. Whether it's a world or a relationship…Everything has its time. And everything ends._

_-Sarah Jane Smith_

Clary listed against Jace, the rocking of the Tardis lolling her into a sleep. She hadn't realized how long she had gone without sleep. True, there had been that small nap right before they had entered Alicante and found the Instruments, but it didn't seem nearly enough. Amy was right, time didn't work the same in the Tardis, and it was just something you had to get used to. At her side, Jace pulled her against him and ran his hand through her hair comfortingly.

"What do you think he's going to do?" asked Clary softly, almost so softly Jace didn't hear. "I mean with Jonathan; what's he going to do with Jonathan?"

Jace frowned at the thought of his step-brother. "I don't know. He won't kill him, he's said as much, but can he keep him around here? I mean, Jonathan hates us both, and he's more than half demon."

Part of Clary had wanted Jace to say that the Doctor would fix Jonathan and everything would be alright, but what was _alright _at this point? There had been war, there had been death, there had been pain and suffering, and now the Doctor was going to make it okay? "He's my brother."

"You don't need to think like that, Clary," Jace answered. "No one will think any less of you if you don't forgive Jonathan. After everything he did to you-to us-no one will blame you if you don't like him"

_The Doctor will blame me,_ Clary thought, thinking of his glowing green eyes, how they seemed to darken when he had looked down upon Jonathan. The Doctor had wanted Jonathan to get better, and though she didn't know why, it had been there. _Would the Doctor forgive me got not forgiving Jonathan, or would he be furious with me? After everything he gave me, after everything he showed me, don't I owe him something? _

"But I keep thinking about what Valentine did to us, Jace, and what if that's what it's like for Jonathan?" Clary turned to face Jace and her eyes were burning. "The Doctor said he was going to fix everything wrong Valentine had done, and what if Jonathan is just one of those wrong things?"

Jace grit his teeth. "I don't know if I have it in me to forgive him, Clary."

Clary nodded against his side. "Do you think he could ever help us?" Clary asked, thinking of the boy who had been so deep in Valentine's council. "If Jonathan ever did turn to us he could prove a useful ally."

"The question is really if Jonathan has it in him to help us," said Jace. "He's a thing of the dark, Clary. Jonathan's very nature would have to change for him to be of any use to us."

"He just knew so much…" Clary mumbled.

Jace leaned back against the headboard of the bed they shared and pulled Clary down beside him. Jace had begun to like the constant rumble that was heard and felt throughout the Tardis. It made him feel like he was going somewhere, like he was always _doing_ something. Deep down was the feeling of wonder, something Jace hadn't felt in years, not since his father had quashed whatever wonder there was in the world; the Doctor had brought wonder back into his life.

"He can only help us so far as his knowledge of Valentine's plans for us, but that knowledge doesn't matter much for us now. We have the Mortal Instruments, we don't need anything else."

"What is the Doctor going to do-?" A loud knock cut Clary off and she stared up at the door; she glanced at Jace and he shrugged. "Come in!"

The door slid back and Max came pelting into the room, Isabelle trying to rush after him. Max bounded onto the bed. "I heard River, Amy, and Rory speaking, and they're going to try and make a new Cup as soon as the Doctor is done with Jonathan!"

"Max, didn't I tell you not to interrupt them?" Isabelle asked, coming up behind him and frowning.

"I don't remember you saying that," Max shrugged. His eyes were glowing when he looked at Jace. "Are we going to rescue our parents and free them from Valentine?"

"Yes, we are," Jace promised. "The Doctor is going to help us and we're going to remake the Cup." When Jace realized how much trust he had placed in a man he hardly knew, he swallowed loudly. "He said he would."

Isabelle perched herself on the edge of the bed, looking between Jace and Clary meaningfully. "So when are we going to do it? I mean, we've just been sitting around for a day while the Doctor locks himself up with Jonathan. I'd like to have a plan."

"The Doctor is not really the planning sort of guy," Clary hedged. "We've got the Instruments, and we're in a time machine. All we have to do is remake the Cup and we can go back to Idris at anytime and begin to free the shadowhunters."

"I'd like if we could start that _now_," Isabelle sighed. "I feel like we're just sitting around doing nothing while Valentine plans for war. What has he done by now? He must have thought of some counter attack?"

"The Doctor explained it," said Clary slowly. "He said that the time stream that we're in now will cease to exist when we go back in time. I wouldn't worry about what's happening now."

Max glanced at Jace, searching his face for any sign of conformation. "Since he's a time traveler, the Doctor doesn't really see time like we do; he has all the time in the universe to make things right."

* * *

"That's it," said the Doctor, watching the small drops of blackish red blood dribble out of Jonathan's arm. "That's all the blood I'll need."

Jonathan watched the Doctor while he studied the boy's blood. "Well, I'm glad you're pleased with it. How long is it going to take for you to test it?"

"Maybe ten minutes," shrugged the Doctor. "I'm not too worried about what I'm going to find; I already know. The real question is what are you going to do now that you're free from Lilith's grip?"

"You have an idea for me?" asked Jonathan.

"We're going to remake the Cup and reverse the effects it has on the shadowhunters. It could be very useful to have a way of putting Valentine out of commission. You could help with that." The Doctor looked Jonathan over. "I'm sure your family would be very grateful."

"Jocelyn loves Valentine."

"I meant Clary and Jace." The Doctor saw a shadow pass through Jonathan's eyes. "They don't hate you, Jonathan; it's just that you have to give them a reason to trust you."

"It's not my fault I was the way I was," Jonathan muttered, slouching down in his bed. "You told them that, didn't you?"

"Yes, of course," said the Doctor defensively. "And they trust that I'm acting in their best interests. They may not like you much, but they'll suffer your presence for me."

"That does make me feel so much better," Jonathan said sardonically, but a small part of him wondered if Clary and Jace could ever really trust him. However, it was quickly quashed by his own bitterness. "I might not be a demon, but I still don't like them."

The Doctor fixed him with one of those clear-eyed stares, too powerful for him to turn away. "You don't have to like them, Jonathan, but they're still your family, and that means that no matter what they do or say or think, you'll be there for them. Now it's more important than ever."

"Why?" Jonathan asked. "You don't need my help to stop Valentine; you have a plan already, and the Tardis is the perfect prison for him while you work on the Cup and fixing the shadowhunters."

"It's not Valentine I'm worried about," the Doctor finally said. "I know we can handle him well. No, what I'm concerned with the time paradox; it caused all this in the first place, and I can't leave until it's sorted out." When Jonathan continued to stare, nonplussed, the Doctor explain the idea of a time paradox and how something had upset time resulting in Valentine winning the war. "It's going to be difficult to fix this, and even now, after saving you and stopping Valentine, I don't know if it's enough to offset it."

"Do you know what caused the paradox?" Jonathan asked.

The Doctor turned away and Jonathan didn't miss the pain his eyes. "Yes, yes I know what caused it."

"Then just go fix that."

"It won't be that easy," the Doctor murmured, and then smile up at Jonathan. "It's time I let the others know, though. Come with me, Jonathan; now that you're on our side it's time you came to the meetings."

Jonathan swung his legs around and off the bed, and carefully tested his weight on his feet. It was a bit unsteady, but he managed to stumble after the Doctor. When they left his room, Jonathan checked on the spot of the long corridors that stretched out before him, the flashing lights, and the groaning and moaning of the Tardis. A small part of him had refused to believe that he was actually on a time machine, but this view pushed it out of his mind. Following the Doctor, Jonathan made his uncertain way through the Tardis and to the main control room. As he expected, there were quite a lot of outraged cries when he entered the room.

"Get back!" Alec ordered to both Isabelle and Max. Magnus had jumped up as well.

Jace and Clary, who had come back to the control room to see if the Doctor had started fixing the Cup, both jumped up and drew what little weapons they had. Jace, of course, pushed Clary behind him and prepared for whatever attack Jonathan had planned. Amy and Rory both blinked politely and behind them, River snorted into her hand.

"He's just a _boy_," River practically giggled.

Jace didn't appreciate River's levity. "He's a half-demon monster who helped Valentine imprison us all."

"Only half right, Jace," the Doctor proclaimed, coming into view. "He is a monster who helped Valentine imprison you all-" The Doctor paused, considering what he had just said, shrugged, and continued "-but he's _not _half-demon. And that's the important thing to remember."

From behind Jace, Clary gave Jonathan a considering look. He certainly seemed to be doing his best to look innocent and diminished. His hands were clasped casually before him, and he kept his gaze down. His lips, top, were frowning with contrition. It could all have been an act, after all, Valentine had trained Jonathan to be a good actor, but she got a strange feeling from Jonathan. He seemed less possessed of his dark energy.

"And it's very lucky he is, too, because we've got some work cut out for us and Jonathan is going to prove useful," the Doctor went on, nudging Jonathan down the stairs to join the small gathering. They drew back from him in fear.

"Maybe I don't belong here," Jonathan murmured to the Doctor over his shoulder. "Are you sure don't have a cell somewhere you can put me? It might make everyone a bit more comfortable."

"Don't be ridiculous," the Doctor sighed, "if I put you in a cell we'd have to have these talks down in the basement, and it cold and dark down there; we'd hardly be comfortable."

Jonathan raised an eyebrow but shrugged. "As long as you're sure."

"We're not!" Isabelle snapped, giving the Doctor a hard look.

"You're fine," the Doctor said, heading towards the controls of the Tardis and gesturing Jonathan to follow him. "River fixed the Temporal Grace Unit, so it's not like Jonathan can actually do anything to you. Now, we've got some business to discuss."

"Have you started fixing the Cup?" Clary asked, still not taking her eyes off Jonathan.

"Well, no," the Doctor admitted. "I've been having a nice long chat with Jonathan, filling him in, and now, though I really do hate to, I've got to do some filling in with you."

"There's more?" Jace said with disgust. "I thought we'd covered the time paradox, the alternate time stream, and how to go about fixing it. What else is there?"

The Doctor looked over to River, and she nodded firmly. Clary saw the exchange and felt an unpleasant feeling in her stomach. _What have they been keeping from us? _

"What is it, Doctor?" Clary asked, drawing his attention back to them. "What haven't you told us?"

"I know what caused the time paradox," the Doctor said softly, staring down into his hands. "The event that should have happened but didn't."

There was a perceptible pause, and then Jace laughed. "Then this is good, right? If you know what happened, it's not a shot in the dark anymore. We can just resolve it and move on."

"It's not that simple, Jace," River said before the Doctor had a chance to speak. "Time is complicated, and events that should happen that didn't aren't always bad. Sometimes, things happen, and they're good, but they just cause bad things to happen."

"Well," Isabelle said irritable. "What's this event then? Is it good or bad?"

"It let Valentine win," Alec grumbled. "I hardly think it can be good, whatever it is."

"I thought time paradoxes resolved themselves?" Clary asked loudly, staring at the Doctor. "You said that, you said that a lot of times the paradox just fixes itself either by setting into action a series of events that equals it in magnitude, or the events it causes, cause it to happen anyway."

"Clary, this isn't something that we necessarily _want _to resolve itself," he hedged. "If we have the chance, I think we should try and find a way to keep ourselves on this track."

"Then how do we fix Idris and the shadowhunters?" Isabelle demanded.

"And what is this event?" Magnus asked sharply, his cat eyes scrutinizing the Doctor. He had been alive a long time, and he had seen many different types of men-many different types of liars. He knew when someone was avoiding him. "For so long you've been saying that to resolve the paradox is to fix the war. Now, suddenly, you want us to gloss over it and move on. What caused the paradox?"

"It's not his fault!" the Doctor said frantically.

"_His_ fault?" Jace pressed, and his eyes moved unerringly to Jonathan. "Jonathan _was _supposed to die! I should have killed him in the valley, shouldn't I?"

"Yes, but that's not-"

"Then why is he still alive?" Isabelle was glaring at Jonathan, and his eyebrows moved up in surprise, having not really had her fury directed at him. "Why did you let him live when it's ruined everything?"

"Jonathan's death isn't the cause of the paradox," the Doctor shot back at her.

"You said he was supposed to die," Alec returned, giving Jonathan a considering look. "He should have died but here he is." Then he added softly, "It can't hurt to kill him."

The Doctor eyes grew very large-in shock-but then narrowed to furious slits. Alec had never had such a powerful anger directed at him and he swallowed. "It can't _hurt _to kill him? I think it would hurt him a great deal!"

"After everything he did, though," Isabelle pressed, holding Max tightly against her. "Jonathan, if you really are free of the demon's grip you must see-"

"That I should die?" Jonathan growled, and his eyes darkened. "Don't you think it's a little unfair?"

"We're talking about an entire race!" Alec snarled at him.

"An entire race of people who hate me," Jonathan smirked. "I'm even less inclined to save them."

"Then you're not changed at all," Jace said, his eyes burning. "Any one of us would be willing to sacrifice-"

"Oh, that's rich!" Jonathan snarled, and he felt a tremor in his hand; he itched for a weapon.

"No one is sacrificing anything!" the Doctor cried above the tumult. The shadowhunters looked up to him, feeling a pulse of power radiate through the air. "I didn't bring Jonathan here just so we could kill him."

"That's not how we do things here," Amy aid coldly, staring down each of them in turn. "I mean, what kind of people are you? Jonathan's a boy and you want to go killing him? You're mad!"

Clary felt her eyes drop with shame and somewhere in her a voice said, _You want to kill your own brother; that's revolting. You're sick._

"But we need to fix time," Alec finally said. "If we're going to set this world back to rights then we need to start with the paradox."

"And did I say Jonathan was the paradox?" the Doctor said evenly.

Alec's mouth went dry, but Isabelle picked up. "He was supposed to have died, you said."

"In the words of one of my favorite authors, 'Many that live deserve death. And some that die deserve life. Can you give it to them?'" When Isabelle's mouth snapped shut and her eyes dropped, the Doctor looked grim. "Perhaps it is time I explained this paradox."

"Perhaps you should," Jace said a little sharply. "Since it seems we're about to tear each other apart."

The Doctor ran and hand through his hair, looking distracted. "Jace _was _supposed to kill Jonathan in the valley; had he done that, he would have then gone to find Valentine preparing to summon the Angel." Jace's face dropped, and Clary whispered gently to him not to feel guilty. "Don't, Jace; when you arrived at Lake Lyn, you would have made to kill Valentine, and instead, he would have killed you, and used your blood to summon the Angel."

"But that's what happened," Clary said. "I mean, Jace wasn't there, but Valentine still raised the Angel."

"True," the Doctor shrugged, and then launched into his explanation. "Had he raised the Angel, Clary, desperate to avenge you, would have broken the seal binding the Angel. The Angel's allegiance would have shifted to Clary. It killed Valentine and then granted her one wish instead. And do you know what that one wish was?" The Doctor smiled kindly down on the two of them.

"Jace," Clary whispered.

"That's right," the Doctor said briskly, and began pacing in his usual manner.

"But I don't understand," Clary said, clutching Jace's hand. "Wouldn't it have been alright then? Valentine and Jonathan dead, everyone else alive?" At the mention of her dead brother, Clary flushed a little; Jonathan noticed.

"Yes," the Doctor admitted, "but not for long. Lilith, the demoness who gave her blood to make Jonathan what he was planned to resurrect his body, using Jace as a form of counterweight. You see, you had raised Jace for 'good' and so she could raise Jonathan for 'evil'. In effect, Jace and Jonathan were bound together, and Jonathan, being the more dominant of the two, would have overpowered Jace and bent him to his will."

Jace looked up now, and his eyes were widened in surprise. "Bound to Jonathan?"

"Oh, yes," said the Doctor slowly. "Your souls would have been intertwined, and the only way to sever them was through death. The war that followed would have been the most horrible the shadowhunters had ever experienced; men, women, children would have died, slaughtered by the demon army Jonathan would raise. Then, true sacrifice would have had to be made, and, if you're curious, it would have been Jonathan who did it." Jonathan's sharp, dark eyes moved to the Doctor.

"As you can see, though, Jace did not die, Lilith could not raise Jonathan, and he never began his ultimate war." The Doctor looked pleased with the looks of shock on the shadowhunters faces. "So, Jonathan's living, ultimately spared thousands of lives."

"This is good then," Isabelle murmured. "The paradox-"

The Doctor slammed his hand down, frustrated. "Jonathan's life is not the paradox!"

"Then what is?" asked Jace slowly. "If Jonathan living is good, but the paradox is bad, can't we just go correct the paradox now?"

"I don't think you can," the Doctor said simply, and he gave Jace and long searching look.

"Why?" asked Jace.

"Because," and it was Magnus, and he was looking very worried, "the Doctor said Jonathan is not the paradox, and if he is not, but his death is instrumental in this, than something else was supposed to happen. Something closely linked to Jonathan's dying in the valley by Jace's hand."

The children looked from Magnus and back to the Doctor. Max, who was now being hugged so tightly, was drawing rasping breaths. "Is it true?" Alec asked.

The Doctor took a long time in answering, when he did, his voice was quiet. "It wasn't Jace alone who killed Jonathan." When they stared at him, he finally looked up and his eyes were bright. "I'm sorry, I'm so sorry.

"Isabelle helped Jace kill Jonathan in the valley. She was furious, you see, bent on revenge, because Jonathan had hurt her." The Doctor shook his head. "When Valentine's army attacked Alicante, Jonathan killed Max."

His statement settled over the crowd like a blanket, and no one seemed to be able to put thoughts into words. On her lap, Max suddenly felt all the excitement and curiosity pass out of him like a balloon deflating; this wasn't much fun anymore. Isabelle and Alec squeezed together, trying to clutch Max protectively between them. Jace felt it like a blow, and he sank onto the grate floor of the Tardis; Clary's hand was still in his and she went down with him, holding him against her. Jonathan, alone, looked nonplussed; he turned to the Doctor.

"I killed Max?"

"You were supposed to," the Doctor nodded. "For whatever reason, you didn't, and because you didn't, Isabelle never felt the urge to run after you and help Jace kill you. It was an oddly fortuitous event, if ever there was one. You all got to live, and the war Lilith planned against mankind never came to be. Interesting how these things happen, isn't it?"

Isabelle was holding Max tighter than ever, and he gave a small, dry sob. "I'm supposed to be dead," he squeaked, and looked desperately between Isabelle, Alec, and Jace. "I was supposed to die?"

"But you didn't," the Doctor said firmly. "You lived, and thousands of innocents were saved because of it."

"Well-well, what does this mean for us?" Isabelle asked, covering Max's face. "What do we do know?"

"We're going to do what we planned on doing," the Doctor answered gravely. "We're going to lure Valentine onto the Tardis-where he'll be unable to do any damage-then, we'll rebuild the Cup, reverse the effects, and free the shadowhunters. Easy enough, I think."

"Is Max in danger?" Alec asked. "Is Max in danger of dying?"

The Doctor frowned thoughtfully. "Probably not, but it will be best if we keep him away from the fray. Paradoxes do have a way of resolving themselves."

"Will he be safe on the Tardis?" Alec asked.

"Safest place he could be," the Doctor assured, but he saw how pale Isabelle's face was. The Doctor was pausing, thinking fast, wondering just how much danger Max was in. Slowly, his eyes moved over to Jace, who was staring at Max like a hawk. "But, maybe someone should stay behind."


	18. Traitor

Traitor

_No. We don't walk away. But, when we're holding on to something precious, we run. We run and run as fast as we can and we don't stop running until we are out from under the shadow._

_-The Doctor_

The Tardis was shaking in its usual manner, tossing the passengers back and forth, when Jace felt a gentle hand on his back. He expected it to be Clary, but when he turned, he saw that Clary was on the other side of room, seated between Amy and Rory, speaking to them excitedly about their own adventures with the Doctor. No, behind him was River, and she smiled kindly and winked. Jace swallowed a bit louder than he meant; River was a formidable woman and anything she had to say was probably fraught with danger, if not bad news.

"What is it?"

River lowered her voice. "The Doctor wanted to talk to you for a little bit, Jace. Just a quick overview of the plan; you know how the others follow you."

Jace was a little gratified that the Doctor thought that his friends trusted him enough to follow his lead. He smiled a bit to himself and let River lead him up to where the Doctor was monitoring the Tardis controls. When he saw River and Jace approaching, he drew back, his face serious again. He leaned a bit to the side, and Jace saw that Jonathan was seated quietly by his side. When he saw Jace, his lips turned down in a frown.

"You wanted to speak with me, Doctor?" Jace asked, trying to ignore Jonathan as best he could.

"Yes, yes, there were some things that we needed to discuss, and I thought discretion was best in this case." His eyes moved from Jace to Isabelle, who was in discussion with Magnus. "I'm speaking, of course, about Max."

Jace tensed. "What about him? I thought you said that Max was safe."

The Doctor frowned. "Technically, he should be, but, as I said, time paradoxes have ways of working themselves out, and I would like to ensure that Max goes unharmed during this attack."

"What are you suggesting?" Jace asked, leaning in so their conversation could be quieter.

"Someone should stay with Max to make sure that no undue harm comes his way. The universe is trying to correct his death, and it can come in any form. I think that leaves us with two options."

"Just two?" Jace pressed.

"Whoever stays with Max should be an accomplished fighter as well as safe from most of Valentine's madness. If he's left with Isabelle or Alec, they can defend him, but nearly so well as you; and, if Valentine were to come, I think you would stand some chance of convincing him-at least for a short time-not to do the boy harm."

"I should be out there fighting!" Jace hissed, trying to temper himself. "This is all my fault, and I need to be there to make it right."

"I thought you might say that, Jace," the Doctor said indifferently. "Luckily, there is one person who can stand in for you with Max. That is, though, only if Max's siblings consent."

"Who?"

The Doctor jerked his head back. "Jonathan, of course."

His statement was met with Jace's outright refusal and Jonathan's surprised, frankly unpleasant, face. "I'm not leaving my little brother with the man who wanted to kill him. He'll try and kill him again, or-or give him to Valentine."

"I don't think so," the Doctor said, and Jace saw that his eyes had darkened again, like they always did when he was angry or frustrated. "I think you're making some rather cruel assumptions."

"Well, you're the one who told me Jonathan was going to kill Max," Jace pointed out.

"He didn't, though," the Doctor said, and would have continued, but Jonathan held up a hand.

"Who said I wanted to watch the brat anyway?" Jonathan demanded, and his eyes glinted. "Just because I can look after some kid-_without _hurting him, I'd like to remind you-doesn't mean I'm interested in doing it. I don't owe you and your friends anything."

"We took you from Valentine," Jace snapped indignantly.

"I didn't ask you to," Jonathan reminded. "And where exactly do you stand on the whole matter, anyway? First, you don't want me here, and the Doctor brings me and your throw a fit and want to kill me. Now, you want me to be grateful you took me on."

"That's not what I meant," Jace growled. "I don't want you here and I don't want you watching my brother."

"Well, what do you want with me?" Jonathan suddenly snarled. "If I'm dead, I can't help you, but if I'm alive, you want me dead. What's it going to be, little brother?"

"Don't call me that!" Jace hissed.

"Hey, let's take a breather-" the Doctor began.

"You're a royal hypocrite, you know that?" Jonathan continued, smiling like an angel. "You call me a monster, but at least I don't pretend to be something I'm not."

"I'm not pretending!"

"Alright you two, wait a minute-" The Doctor was getting a little desperate now, and he looked like he was drowning in the step-brothers anger.

"Yes, you are," Jonathan said quickly. "You're pretending to be some good, sweet, helpless Angel Boy, but this whole time, you're sitting across from me, hoping I'll die."

"You want us dead," Jace replied.

"But I don't pretend that I don't," Jonathan said smugly.

"Stop it now!" the Doctor crowed, throwing his hands up and turning on the spot; he almost looked like he was dancing between them. Jace snapped his mouth shut and Jonathan politely smiled. "Are you sure you're not brothers, because you bloody well argue like them!"

"We just don't always see eye to eye, and have a nasty knack for pushing each other's temper," Jonathan answered courteously, but his smile was like a razor and his eyes were still on Jace's face. "Please, continue."

The Doctor's eyes moved to Jace who was breathing hard, but he nodded and said, "What do you suggest we do then?"

"I think you should stay here once we get Valentine on board, Jace," said the Doctor. "I need you to stay and guard Max and keep an eye on Valentine."

Jace looked very unhappy about the whole situation. "Why do I have to stay with him?"

"Who else is going to protect him?" the Doctor challenged, "and who else could stop Valentine if he tries to escape? You're the only person here aside from Jonathan who has the training to fight him."

Jace was very displeased with the whole idea. He was frowning rather impressively, at least. "Why does someone have to stay on the Tardis with him anyway? Can't I take Max somewhere safe in Idris?"

"No, the safest place in the universe is the Tardis, and I'm not going to leave him alone." The Doctor turned to the controls and showed Jace the screen he was using to steer. Jace was surprised to see the planet earth coming into view. "We're going to land soon, and once we do, things are going to move quickly. Jonathan has agreed to help us convince Valentine to come on board; now, I think you can do your part."

"I don't want to be missing from the battle," Jace finally admitted.

"There isn't going to be a battle," the Doctor said quickly. "Not if I can help it. We're going to lure Valentine on board and then we'll have all the free time to cure the shadowhunters."

It was a painful moment for Jace, and it wasn't helped much by Jonathan's calm, sneering face. Jace was going to be left behind to watch Max while all his friends went to fight the battle. Even worse, _Jonathan _got to go and fight. It was the turning point of the war, the defining moment of the shadowhunter nation, and he was going to be sitting in the Tardis, babysitting Max.

_He's still in danger, Jace, and you would never forgive yourself if he died_, Jace thought bitterly. "It's just not…fair."

"Some things," the Doctor said, gripping his shoulder comfortingly, "are worth more than pride and honor. There are some things that we lay down our lives for, but then there are others that we lay down _everything _for. No one is going to question your motives, Jace; we all know who you are and what you're fighting for."

Jace bowed his head to the inevitable. "I'll stay with Max," he finally said. "I'll keep an eye on Valentine, too, but promise me you'll watch Clary."

The Doctor looked pleased. "I'm sure Max will be happy you're staying behind; he seems very attached to you. Now, get your friends ready, we're going to land in a few minutes."

* * *

_Jonathan gone, Jace and Clary gone, the Instruments gone, and not even the slightest inkling of where they went. _Valentine slammed his hand down on his desk, grinding the papers in his hands. _When I find the Doctor I'm going to kill him._

The last twenty-four hours, the hours following Jonathan's abduction, had been a nightmare. Jocelyn wouldn't leave him be, panicking about their children, the Clave was at a stand-still, word had gotten out of the Lightwood children's escape, he had no leads as to where his children had gone, and, to make matter much worse, countless demons he had set as sentries to guard Alicante had vanished into the night and no matter how he tried, Valentine couldn't summon them back. His anger had gotten the better of him, and though he tried his best not to let the mask of control and unruffled dignity slip, he was becoming desperate to make an attack. Slowly, almost like a snake, he rose from his desk and strolled slowly to the fireplace where he leaned against the mantle, massaging his forehead.

"So, where have you taken my children, Doctor?" Valentine asked aloud, considering all the possibilities. It was a little disconcerting that they had somehow managed to overpower and contain Jonathan; he wished desperately his demon army was still in his control, but not only were the Mortal Instruments gone, the demons were as well. "How are you staying out of my grasp?"

"It's his Tardis," said a voice from the door.

Valentine's head shot up, and he had to hold back a very startled gasp at the sight of his son. Jonathan looked…different. There was something about his demeanor, it was more powerful, more determined, more steely than usual. Valentine was rather impressed by the sight of Jonathan, but he didn't let it show on his face. Instead, he narrowed his eyes in contemplation.

"Jonathan," he said conversationally, "you've returned?"

"Escaped," he corrected, a smile sliding into place on his handsome face. "The Doctor, Jace, and Clary have the Instruments, and they remade them so they could use them against us. The Doctor landed his machine on the outskirts of the city, just inside the wards; he was planning on cornering you and forcing you to surrender."

"Planning on it?" Valentine asked softly.

Jonathan's smile widened wickedly. "Well, the Doctor has a nasty habit of trying to save lives-most unfortunately, mine. He didn't let Jace kill me, so, when they landed and were preparing to leave, I attacked." Jonathan examined his hands speculatively. "I didn't kill Jace or Clary, they're still alive and bound on the Tardis. The Doctor and his human friends, though, they're dead."

Valentine raised an eyebrow. Jonathan's manner seemed the same as ever, but, after Jonathan's sudden illness, he didn't know that he could trust him implicitly. "You say Jace and Clary are on his ship?"

"Well, I wasn't going to carry them all the way back here on my own, was I?" Jonathan looked scandalized. "Besides, I figured that if Jace woke up he'd put up a fight; you can probably guess he doesn't want to come back home."

"Indeed," Valentine agreed. "So, tell me, this Doctor, he's dead?"

"So far as I know," shrugged Jonathan. "A man is usually dead when you slit his throat-no matter what planet you're from."

"And he didn't put up a fight?" Valentine ran his eyes over Jonathan's seemingly composed form.

"A bit," admitted Jonathan, "but he's a very non-violent man. He doesn't even carry a weapon, he's got a screwdriver he uses to fix things, that's all. He did look ready to kill me after I finished off his little red-head, but…he never got around to stopping me."

"I would have thought Jace would have put up a fight," Valentine reasoned. "No matter how gifted a warrior you are, I think Jace would have slowed you up."

Jonathan raised his finger. "He _would _but I got to Clary before he could. Jace wasn't in any position to fight when I had his girlfriend at my mercy."

Valentine nodded slowly. "So, where is this Doctor's…what did you call it?"

"The Tardis," said Jonathan quickly. "It's his time machine, disguised as a blue telephone box; it's just within the city. I thought you might like to see it."

Valentine prowled around his desk and paused before Jonathan. "You said that the Doctor remade the Instruments, but where are they?"

"On the Tardis somewhere," Jonathan said after a beat. "I was kept in a bedroom for my stay; I didn't get to see much of the goings on. I thought we could search for it, or interrogate Clary and Jace. I'm sure the brats know where it is."

"And the Lightwoods?" Valentine pressed, his eyes glinting. "What became of the Lightwood children?"

"Ah," here Jonathan assembled his face into something regretful. "Well, they were trying to stop me killing the Doctor, and then there was the whole struggle with Jace. I couldn't let them help him…I'm afraid they're quite dead."

Valentine seemed slightly amused by his answer. "Ah, well, there is little to be done for it, bad blood is bad blood, after all. Take me this Tardis."

Jonathan bowed his head graciously, smiling slightly. "Follow me, Father."

Valentine wasn't sure if he trusted Jonathan quite yet, and he couldn't forget the way Jonathan had collapsed before him in pain. Perhaps there was something more to this, perhaps Jonathan wasn't all he seemed, but regardless, Valentine needed to see this Tardis, and he needed to meet the Doctor. Even if Jonathan had betrayed him, Valentine needed to finally meet this man face to face.

They left the house in the city circle quickly, under cover of evening shadow, and made their way swiftly through the city. As they approached the outside of the city, Valentine saw a small box on the horizon, and wondered at it because it seemed so out of place. As they drew nearer, details of the box came into focus: the blue, the words _Police Call Box_, and sign with scribbling on the front door. It seemed to Valentine a helpless, harmless object.

"This is the time machine?" Valentine asked, staring hard at the box.

"Yes, Father; it's not what it seems." To Jonathan, he suddenly noticed how strange this all must seem, and how suspicious it was to his father. "It's much larger on the inside, and there's strange technology, and writing-writing in a language I've never seen. It's not human, whatever it is."

Valentine nodded and said nothing more until they stood before the Tardis. He examined it from a distance, circling the box and never blinking. It was just a box, a wooden, painted box. Carefully, Valentine withdrew a stele and then sliced sharply up. He saw, though, that the Tardis looked completely unharmed; there wasn't a scratch or dent, not a mark to be seen. Valentine pressed his lips together and returned to Jonathan.

"It's a disguise."

Jonathan nodded simply. "Yes, the Doctor said as much. It's open, too, if you'd like to see inside?"

"I would very much like to see where Jace and Clary have been hiding these last few days." Valentine had put his weapon away, but his fingers rested gently on the hilt, ready to draw it if need be. "I trust they're still bound."

"If I know how to tie a knot they should be," Jonathan replied sullenly at his father's mistrust. "Here, follow me."

Jonathan pushed the door to the Tardis open and strutted through, chin up and a smug smile on his face. He called out, "Wake up you miserable lot, we've got a guest!" Hearing this, Valentine followed.

Valentine had a fleeting look of the inside of the Tardis, and it was enough to draw him up short. Up until then, he hadn't quite believed in the whole story of a time traveling, space ship. Now, faced with the immensity of the interior of the Tardis, with the flashing lights, the whirring, the shaking, and the cold metal, he didn't know how to put into words what he wanted to say. His eyes took it all in seamlessly, however, his mind didn't really process it. No, his gaze was quickly drawn to the figure standing a few yards away, a young man with dark hair and strange green eyes. When he saw Valentine, he smiled graciously.

"Welcome aboard, Valentine," he said in an even voice, and his eyes flicked over his form. "Do you like my Tardis?"

"Traitor," Valentine said softly to Jonathan.

"I wouldn't call him a traitor, Valentine, so fast. You're the father who traded him to a demon for a weapon," the man-the Doctor-said. "I dare say you'd have a lot of explaining to do."

"Not to you, Doctor," said Valentine, feeling along the hilt of the weapon. "Regardless of the fact that my son had betrayed me, I'm here now, and I think you and I have a bit to discuss."

The Doctor smiled. "I'd love to have a chat, but I've got a planet to save."

"Oh, do you?" said Valentine curiously. "You'll find that rather hard to do after I've had a say." Then, before anyone could move to stop him, Valentine jerked the blade from his pocket and aimed it at the Doctor. The blade flew through the air, directly at the Doctor's heart-

-and it missed.

Valentine gave a start because he was suddenly alone in the Tardis. He spun about, and Jonathan was gone, the Doctor was gone, the lights that had one moment before been flashing, were off. The room was completely empty of everything and everyone in the blink of an eye. Carefully, Valentine took a few steps in the direction of the controls, but nothing happened. A few more, and still no change, so he launched himself at the controls, banging on them furiously.

"Doctor!" he cried. "Doctor, you coward, come out! Stop hiding behind your Tardis and face me." No one answered him, and his face contorted furiously. "Jonathan! Jace!" He slammed his hand down on the controls and screen before him flashed into life.

"Valentine!" It was the Doctor, and he was waving merrily at him. Behind him, Valentine saw not only Jonathan, but Jace and Clary as well. However, he noticed, with an odd sinking feeling, that he could also see the room behind them, and it was the _exact room_ he was standing in then. How could he been in the same room as the Doctor, and yet not see him?

"What have you done?" Valentine growled.

"Ah, yes, that," the Doctor said, fussing with his bowtie. "Well, that's actually you, Valentine. See, the Tardis has something called a Temporal Grace Unit, and it means that, while on the Tardis, all weapons are harmless. It's quite impossible to hurt someone while you're on the Tardis."

"Where am I?" Valentine said sharply, ignoring what the Doctor had said.

"Defense system of the Tardis," shrugged the Doctor. "The Tardis is a time machine, and, as such, the interior of the Tardis is in flux, too. You're in the Tardis, but, because you posed a threat to its inhabitants, it transported you to the Tardis in another point in time. Imagine…a time capsule, and you're trapped inside it until you lay down your arms."

Valentine's eyes glinted. "You can't leave me in here."

"I can," said the Doctor with a rather serious look. "Now, please, feel free to wander about the Tardis. I don't think you're going to find much, though. I think you're about a hundred years in the past from where we are now."

"_What_?" Valentine hissed through his teeth. "What do you mean-"

But the Doctor waved at him, his gaze shifting off to something on his side of the screen. "Listen, Valentine, we've got to go; got a civilization to save. We'll tell you how it goes when we get back!" He winked jollily and whisked off.

"Come back!" Valentine snarled. "Doctor, come back!"

But it was too late, the Doctor had already jumped from the control panel to join the small gathering of people at the doors to the Tardis. "So," he cried, clapping his hands, "who's ready to go save the world?"

Clary and Amy shared a smile, but Jace looked like he was tired of waiting. "What's the plan?"

"We'll go down to the lake, and I'll help Clary remake the Cup. While we're down there, the Lightwoods, the Ponds, and Magnus will go to Alicante and gather the shadowhunters." The Doctor gave Jace a meaningful look, though, and his eyes shifted to Max, who was standing behind Alec, holding his leg. "I trust you'll be alright here?"

Jace forced a smile for Max, who looked back at him with his usual wonder. "I think we'll manage."

"Right then, shall we head out?" the Doctor looked to the assembled shadowhunter, all of whom were clutching whatever weapons they could salvage and looking very determined. "Here we go!"

Clary spun about and kissed Jace luxuriously before joining the others streaming past him. Jace reached out just a bit, wishing with all his heart he could be by Clary's side that day, but he felt the tentative tug on his shirt, and looked down to see Max staring up at him with big, brown eyes. He blew his breath out in a whistle and ruffled his hair.

"So, Max, what do you want to see?"

Max pressed his lips together. "The Doctor said there's a game room on the Tardis. Do you know where it is?"

"We can find it," Jace shrugged, and though the door to the Tardis was only a few feet away, he turned from it regretfully and led Max away, hand on his shoulder.

* * *

Clary felt an odd prickling at the back of her neck, and took a few rapid steps to get as close as she could to the Doctor. She didn't feel especially safe with Jonathan behind her, even if he had convinced the Doctor he was on their side. _Even if he did help you trick Valentine, _she reminded herself bitterly. She felt her hand brush the Doctor's forearm and he glanced down at her. Clary must have looked nervous because he smiled and winked.

"You alright, Clary? You're looking a bit peeked," he said conversationally.

"I 'm just…" _Just what? Scared of your brother who is about three feet behind you and as likely to kill you as he is to help you? _"I didn't want to leave Jace and Max behind with Valentine, especially since Max was supposed to-well, you know."

"You've got nothing to worry about, Clary," the Doctor assured. "The Tardis will protect Jace and Max; it's got Valentine trapped in another century as it is! He can't get out."

Clary nodded faintly and kept her eyes on the path ahead. In the distance, she could see Lake Lyn glimmering and her heart skipped a beat; this was it, this was how it was all going to end. Almost a year of torture and humiliation, a year of being used and punished, and it was all finally going to end. Life could go back to normal.

After a bit of trekking, they broke through the trees and were standing on the shore of Lake Lyn. Clary cringed a bit, recalling her father's victory on this very spot, and when she paused, Jonathan bumped into her, sending her sprawling into the sand unceremoniously. Blushing and spitting out a bit of sand, Clary felt someone's hand take hers and help her back up to her feet. It was Jonathan.

"Sorry about that, _sis_," he said with a winning smile, but Clary just stared and pulled her hand back slowly. "I wasn't quite paying attention to where I was going. Brings back memories, this place, doesn't it?" His smile stayed in place, but it became strained with some memory.

"Don't worry about it," Clary shrugged, and rushed off after the Doctor

He was examining the water, muttering to himself. "…brilliant really, using the natural deposits in the water to help bind the Instruments together…must be one hell of a hot spring down there…Oh, hello, Clary!" He jumped to his feet gesturing at Lake Lyn. "So, would you like to begin?"

Clary looked uncertainly down at the water than at her hands, as if unsure if she even had it in her to begin. "I'm not sure what rune to use…I thought a-a binding rune or something, to draw the Instruments together again."

"Then that'll be it," agreed the Doctor with an encouraging sort of smile.

Now that is came to it, Clary simply pushed her hair behind her ears and sank onto her knees before the lapping water, trying to envision the rune. The Doctor had plashed the ashes of the Instruments before her so she might be able to draw on them with a stele, and he stood to the side, admiring the archaic technology and wishing a bit for the creations that had been commonplace on Gallifrey. Jonathan, for his part, watched his sister with dark, considering eyes.

_It's not really fair, _he thought. _Everyone gets justice but me; I'm always going to be Valentine's Son, and monster child. Even Clary is afraid of me…_Jonathan's face turned into an ugly frown, and he felt his fingers twitch viciously. _I'm not a demon, but I can still feel anger._

Jonathan's thoughts of betrayal, though, were pushed from his mind at the white light that was growing from before Clary. He saw the ashes of the Instruments swirl a bit, as if in a wind, and they began to spin like water down a drain. This was it, this was the end of Valentine's rein on the shadowhunters. A muscle in Jonathan's jaw worked.

_I've been betrayed…_he thought maliciously, and then began to creep forward, his hands forming fists. _I deserve justice, too. _

Clary was shaking, all her mind focused on the runes drawing the bits of the Instruments together again; it was a tiring sensation, Clary felt like all her energy was being drained from her body. Beside her, the Doctor was completely consumed with the sight before him; it had been a while since he'd seen a human do anything quite so interesting. It hadn't been since Rose had absorbed the Tardis matrix that a human had really done the unthinkable. Jonathan was behind them now, watching as the Cup was formed anew.

For maybe ten seconds, Clary held the new Cup in her hands. She could feel the metal, burning pleasantly in her hands, and her arm vibrated with the power in the Cup. For ten seconds, she felt that unmistakable sense of victory. Then, quite suddenly, something heavy and hard hit the back of her head; she tumbled forward, unconscious. The Doctor turned, giving a cry of shock, but all he saw was Jonathan's face, carved into an ugly look, before his fist connected with the Doctor's head and he knew no more.

Jonathan fled from the lake then, his thoughts racing furiously. _None of its fair, I deserve justice, I deserve to have a life, and there's only way I can do that._

It took a while, but Jonathan was swift and he was driven on by his fury and his desire for revenge. He arrived at the Tardis after half an hour, and, after careful thought and planning, pushed the door open. He walked slowly, all the while, thinking, thinking…

_You can't harm someone on the Tardis…you have to get them off first…_

Jonathan crept soundlessly along, pausing before the kitchen, the library, the pool, always listening for the sound of voices. When he heard the sound of childish laughter, he knew. Carefully, Jonathan opened the door to the game room, peering in. His eyes alighted on the forms of Jace and Max, sitting around a chess board. He smiled, Jace's back was turned to him. One more deep, steadying breath, and Jonathan lunged across the room; he cleared Jace's head in his leap, spun about when his feet touched the ground, and scooped Max up.

"_Jonathan_!" Jace snarled, jumping to his feet.

"Hello, little brother," Jonathan said pleasantly, running his hand over Max's throat. "Hit a little snag in the plan down by the lake, thought I'd come back to salvage it."

"What are you doing?" he demanded, his fists clenched.

"_Not_ hurting Max, as you can see," Jonathan smirked. "You and I both know that if you try and hurt someone on the Tardis, you'll get sucked into some freak time period, and I just can't afford that. So, what I am going to do, is ask you to sit down so I can tie your hands and gag you. If you refuse, I'm afraid I'll have to take little Max with me, and I'll walk _right out the door_."

"I won't let you," Jace snarled, his eyes on Max's frantic face.

Jonathan barked a laugh. "What are you going to do? _Hurt_ me? Temporal Grace acts both ways, Jace. If you try and harm me, you'll be trapped in time. So, _sit_."

Jace was shaking with pent up rage. Jonathan had lied, tricked them, betrayed them _again_. He knew they should have killed him, he knew he should never have let Jonathan go. Every fiber of Jace's being wanted to throttle him, choke the life out of him, but Max was in his arms, trapped. He had sworn to protect Max, and here he was, risking the boy's life. His hands unclenched painfully and he bit his lip.

_You don't have a choice, you can't let the paradox resolve itself like this, _Jace thought. "Okay, I won't fight you, but you have to promise not to hurt Max."

Jonathan watched Jace sit down, holding his hands out so Jonathan could bind them with a few quick runes. Jonathan did just that, and then added a Silencing rune to shut him up. Max struggled a bit, but Jonathan bound him as well. After inspecting his work on Jace, Jonathan pulled the other boy to his feet and smirked his usual smug look.

"So, little brother, how about you and me go find, Father? I'm sure he'll be so pleased to see us."


	19. Freedom

Freedom

_Everybody knows that everybody dies, but not every day.__Not today.__ Some days are special. Some days are so, so blessed. Some days, nobody dies at all. Now and then, every once in a very long while, every day in a million days, when the wind stands fair and the Doctor comes to call, everybody lives._

_-River Song_

The first thing Clary was aware of was the familiar burning of the Cup in her hand. _He didn't take the Cup…Jonathan left me with the Cup._ It was an odd thought, and even though Clary thought it, she didn't quite understand the implications. Her fingers curled around the handle of the Cup, testing it for life. It hummed in response. _We still have the Cup…we can still stop him._

"Doctor!" Clary spat out, opening her eyes and squinting at the bright light of the sun. "Doctor, are you alright?"

"I'm here, Clary," the Doctor groaned sitting up and giving himself a good shake. "Do you still have the Cup?"

Clary weakly lifted the Cup for the Doctor to see and he stared at it. "Hmm. Jonathan didn't take the Cup."

"I don't think that matters," Clary said darkly, and suddenly, a fit of urgency hit her. Jonathan had attacked them and was on the loose. "He could be freeing Valentine right now; we need to stop him-"

"No," the Doctor said simply, dusting the sand out of his hair. "Even if he's gone to free your father, we need to get to Alicante and start converting shadowhunters. Valentine's power is broken; there's nothing left he can do."

"But Jonathan is _with _him!" Clary practically cried. "And Jonathan poses quite a problem. He just tried to kill us!"

"I'm not dead," the Doctor said simply. "You don't appear to be either. No, I don't know why he did what he did, but I don't think Jonathan is a threat to us. We need to go to the city and free the shadowhunters."

"You still trust him?" Clary rasped, hitting the sand around her. "After all he's done and what he just did- right _now_!"

"I didn't say I trusted him," the Doctor corrected, jumping to his feet and rubbing the sore spot on his head where Jonathan had hit him. "I'm just saying that we have much more pressing matters to deal with at the moment."

"What about Jace and Max?" Clary finally asked, sensing the Doctor's set will. "They're on the Tardis."

"He can't hurt them; Temporal Grace, remember." The Doctor reached down and helped Clary to her feet. His eyes landed on the Cup in her hand. "Come on, the sooner we fix the shadowhunters, the sooner this is all over. We'll deal with Jonathan after."

Clary wanted to deal with Jonathan _now_; she wanted to run after him and put an end to his betrayal once and for all. She wasn't even sure how she wanted to deal with Jonathan, but too many times he'd lied, and too many times he'd hurt people. Her eyes must have given away something of what she was thinking, though, because the Doctor gave her a stern look.

"We have to go now, Clary; don't think about Jonathan, you have a world to save."

If Clary had planned to argue, it was soon pointless. The Doctor had taken off, running with speed that might have surprised even her shadowhunter friends. He led her up, away from the Lake and through the woods that flanked it. Every once in a while, the Doctor would call back some words or encouragement, or, more often, point something out that he found interesting. Clary just followed him, her thoughts barely on the Cup in her hands, but on her brother's sinister plans. He could be anywhere then, and he could be doing anything.

_You need to focus on the Cup right now, _she told herself firmly. _You've got to think of all the people who are depending on you. _

They kept going, Clary and the Doctor, and they didn't stop until Clary was thoroughly out of breath. From where they stopped, Clary could see the towers of Alicante gleaming in the distance, and she felt her heard pound. So soon, they would be there, and then, they would have the Cup, and then…then it was over. She turned her eyes unerringly to the Doctor.

"This is it, right?" she asked weakly, clutching the Cup now more tightly than ever. "Once we fix this, the time paradox is resolved and life goes back to the way it should be?"

"Considerably better than how it should be, I would think," the Doctor mused, thinking fleetingly of Lilith and her demons armies.

"I get my mother back," Clary realized for the first time. She had long since dismissed Jocelyn as a puppet of Valentine's, and had closed her heart to her mother. It was the only way to go on living her life with her mother still in it; she couldn't afford to feel anything for the woman who surrendered her to a merciless father. "She'll stop loving Valentine, won't she?"

"His power over her will be broken, yes," the Doctor agreed. He eyed her from the side and saw the tension in her shoulders. Yes, she was nearing her end; Clary needed this to be over. "Well, shall we head down? I'm sure the Lightwoods and the Ponds will have gathered some people up." Clary nodded, and they headed toward Alicante, at, to Clary's relief, a much more relaxed pace. When they passed through the gates of the city, Clary and the Doctor were met with an odd silence. It seemed like Alicante had been emptied.

"Where is everyone?" Clary asked as they crossed a bridge.

"Hopefully, with the Lightwoods," the Doctor hedged. "Lead the way to the Gard."

They increased their pace, and it soon became clear where the citizens of Alicante were. As they broke cover of the buildings and entered the city circle, they were faced with a sizeable crowd. Amy Pond was standing on the rim of a large fountain, and it seemed Magnus had conjured her up a megaphone, because she was screaming into it, blaring out orders about lining up, about being orderly and patient, and about the new Cup. She also threw in a few snide comments about Valentine himself, a few names even Clary gawked at.

"She's got strong opinions," the Doctor shrugged, and then set off through the crowd, pushing people aside and crowing, "Excuse us! Please make way, got the Cup here. Excuse me, I'm the Doctor!"

Clary found herself soon the center of all attention, the eyes of the entire gathered crowd resting on her and the glowing Cup in her hand. She kept her gaze down, but it was worse than the first day of school, and Clary pushed the Doctor a little desperately, wanting to get out of the press of bodies. As she emerged, Isabelle and Alec caught sight of her, and Isabelle dashed forward to meet her in a hug.

"You've got the Cup!" she cried, shaking her a bit. "We've got as many people together as we could, and more are coming now. How did you do it?"

"I just…drew a rune and put it all together," Clary said shakily. "I haven't tried working it yet, so I don't know-"

"You'll use it on us first," Isabelle said firmly. "Alec and I decided we'd be the first to drink from it to show the others is was safe and worked."

"What if you're hurt?" Clary asked quickly. "What if the Cup backfires or poisons you?"

"Then better it's us," Isabelle said indifferently. She dragged Clary to the fountain where Amy was still calling out her orders, and she plucked at her sleeve, drawing her attention. "Give Clary the megaphone; she needs to explain."

"No, Isabelle, wait-"

"This is Clarissa Morgenstern!" Amy called out, and there was an answering hiss. "She made the Cup that's going to free you all. Listen to her!"

Amy tugged Clary up alongside her and thrust the megaphone into her hand with an encouraging nod. Clary gaped at her in mute terror, and swallowed loudly, and the megaphone echoed with the noise; she flushed. "I-I'm Clary, and I think you all know who I am." There was a lot of angry muttering, and the name Valentine's Child was cried out. "Yes, yes, I'm Valentine's daughter, and I'm sure you all hate me, but you've got to hear me out. Please!" Clary could feel herself sweating and her nerves failed her. Nervously, her eyes flickered over to the Doctor, and he was nodding bravely to her. She saw the light in his eyes, the power too. He had come all this way, drug her and Jace along, and she was going to fail now? "I can fix everything, I've made a new Cup, one that will reverse the effects of Valentine's summons. All you have to do is drink from the Cup."

If Clary had hoped there would be a call of agreement and the shadowhunters were gather up and come forward to drink, she was sadly disappointed. Many of them eyed her suspiciously and a few even called her a liar. They had become too accustomed to Valentine's harshness and Jocelyn's blank, friendly smiles; they were unforgiving, that was all.

_They need to trust me, they need to understand,_ Clary thought desperately, her hand gripping the Cup tightly. _Just tell them truth, be passionate and angry and scared just like they are. So far, you're just Valentine's daughter._

"I know you don't want to trust me," Clary began, trembling. "I know you think I'm lying and I'm trying to hurt you, but I telling you-I'm _begging_ you- to hear me out. I'm just like you, my father took me away from my friends and family and he trapped me in the human world and left me there, all because I wouldn't do what he asked. I've been hurt, I've been scared, and I've been angry, but then I met this man." Clary pointed to the Doctor who suddenly looked very uncomfortable. "I didn't trust him at first; I thought he was working for some resistance, I thought he was going to use me to blackmail Valentine, and I thought I'd be punished for it, but I was _wrong_! He saved my life, and the lives of all my friends; he showed me things I'd never _dreamed _could exist, and I'll admit it, I didn't want to come back. I wanted to stay with him and his friends and never come back to this nightmare-but I did!" Clary was breathing fast now, shaking with her energy. "I didn't have to, he wouldn't have made me, but I knew there was something left here that was _worth_ coming back for. So, I did, and I made the Cup, and I'm here now, and I'm terrified out of my wits. Please," Clary closed her eyes a moment and then summed up the rest of her courage, "I'm asking you to listen and believe, and I'm asking you to drink from this Cup, and, most of all, I'm asking for your trust. That's all I want: your trust."

Clary's words rang out across the now silent group, and she saw eyes staring up at her, and mouths slightly agape, and open faces. Slowly, she looked down to her friends, standing by her feet, and she saw they were all smiling brightly. When she lifted her eyes again, there seemed to be a shift in the crowd; the people were mulling about, falling into small, ordered groups. They were lining up, coming forward slowly, looking at her expectantly.

They were willing to trust her.

* * *

Jace could almost feel Max's fear as a physical thing it was so powerful. _He's got every right to be afraid, seeing as in an alternate reality, Jonathan murdered him. But it won't happen this time, I'm not going to let it happen this time._ Jace flashed Max a brave look, a swift smile, but Max's eyes remained large and terrified.

Jonathan was holding Max in what would have been a gentle, protective way, if not for the blank look on his face. He had Max in one arm, holding him just high enough so Max could look over his shoulder and down onto Jace, who was being dragged along unceremoniously on the end of a rope. Jace was watching Max, holding his gaze so the boy wouldn't look away and realize the situation he was in. They were walking toward the control room again, and Jace considered all the choices he had, all the different actions he could take.

No matter how he considered it, though, the situation seemed hopeless. He could still attack Jonathan, but the other boy was right: Jace would be dragged into another time period and trapped there while Jonathan wrecked havoc. All his friends were currently unaware of the trap Jonathan was springing, though perhaps the Doctor and Clary might suspect it, but how could he change anything when he was captive to Jonathan. He ground his teeth, and in his frustration, Jace groaned very loudly. Jonathan turned about, cutting off Max's view of Jace.

"Something wrong, little brother?" he asked politely. "You're looking a little occupied, a little _tied _up; can I help with you something?"

Jace flushed and jerked the rope that held him in place. _Untie me, you coward, that's what you can help me with!_

Jonathan nodded as if he understood Jace's fury. "I'm afraid I don't understand, Jace. Is something not the way you like it? Are you uncomfortable?" Jace threw all his weight against the rope holding him and Jonathan and Max stumbled forward. Jonathan gave an outraged cry. "Worthless brat!"

Max kicked out at Jonathan, trying to break his hold while Jace continued tugging the rope around. In his fall, Jonathan's grip on Max was loosened and Max escaped, running at once to Jace. He had just reached him and began pulling the gag out of Jace's mouth when Jonathan lunged and dragged him kicking and screaming away. Jace spat the gag out and sat up.

"Jonathan's don't hurt him!" he ordered. "Please, he was just trying to help me. Let him go!"

Jonathan was holding Max by his dark, thick hair, staring down at him with a strange, occupied look. "I'm not going to hurt him, Jace; I just want him to stop his struggling and complaining and listen to me for a moment."

"Well, you'll have to forgive him seeing as you killed him," Jace snarled.

For some reason, this upset Jonathan, and he frowned at Jace. "I _didn't _kill him! Isn't it enough for you, Jace? That reality doesn't even exist, but you're holding me accountable for it? How can I be blamed for something I _didn't_ _even do_?"

"You would have," Jace growled.

"And you would have killed me," Jonathan replied swiftly. "Even now, you're considering it, and I haven't even done anything! What do you expect of me, then? That I'll just stand to the side and let you do as you like? Don't I deserve justice?"

"No," Jace spat, staring daggers. "You helped Valentine take over, you lied and betrayed us, and you've spent the past six months torturing me and Clary."

"So, you're going to punish me forever?" Jonathan shot back. "No, I've thought about it, and I've considered all the possibilities, and I know now that there's only one was for me to get justice. There's only one way left that I can live my life and not be guilty of being Valentine's son."

"So you're going to be Valentine's savior?" Jace asked bitterly. "We never should have trusted you; I don't know what the Doctor was thinking when he took you in. People like you never change, people like you will always be undeserving of friends and family."

Jace thought he saw a flickering of pain in Jonathan's eyes, but it was gone almost at once. Jonathan scooped Max up again and tugged Jace's rope until he was on his feet. "People like me?"

"Monsters."

Jonathan shrugged carelessly and turned away, allowing Max his comforting view of Jace again. A small part of him wanted to force the boy to walk before him, taking away whatever strength he had from Jace's presence, but he found he just couldn't bring himself to be so heartless and cruel to such a small child.

"Come on," he finally said, leading Jace away. "Let's go find Valentine."

* * *

"I can't believe it worked," Clary whispered to Amy. "I can't believe they trusted me after everything, and I can't believe that the Cup actually healed them."

Amy eyed Clary and smiled a little to herself. The girl before her was a far throw from the one she had met, huddled on the school steps in the cold, weighed down by fear and pain. "Were you really so surprised, Clary? You made this, you knew what it could do."

Clary smiled ruefully. "I never know…sometimes my runes don't work right."

"You should be proud, Clary," Amy said, and wrapped an arm about her shoulders in a motherly fashion. "You're a true artist now."

A fleeting image of Vincent came to Clary's mind, and she realized she was never going to see him again; it made her both immeasurably happy and sad to know that the adventure with the Doctor seemed to be over, and the thought of the Doctor woke a reminder of Jonathan. "Amy, I need to speak to the Doctor at once."

Frowning, Amy pointed to the Doctor who was seated on the rim of the fountain, looking around in a dazed sort of way. Clary joined him. "We haven't seen Jonathan yet."

"I don't think we will for a while," the Doctor mused. "He probably went to the Tardis, and now he has to come all the way here. It'll be a bit of a roundabout trip for him."

"He could have hurt Jace and Max-"

"We've have this conversation before, Clary," the Doctor said. "He can't hurt anyone on the Tardis, and it's more important that we free the shadowhunters. Jonathan will come to us, and when he does, then we will have to be ready for him."

Clary mulled it over and went to join Isabelle and Alec who were searching for their parents in the crowd. She pulled them aside and whispered quickly what had transpired at the lake. Alec looked grim but collected, Isabelle, however, was furious.

"And you just let him run off? You should have told us before; we would have gone after him."

Clary shrugged. "The Doctor said it's more important to be here than stopping Jonathan from doing nothing. After all, he can't hurt anyone on the Tardis."

"Yeah," Isabelle said slowly, "but I don't like the idea of that monster running around underfoot. Especially with Max there."

"Jace will take care of Max," Clary said with certainty. "You know he would never let anything happen to your brother. I'm just worried about what's going to happen when Jonathan comes here."

"You think he will?"

"I think so," she said, nodding. "I just don't know what he'll try to do once the shadowhunters are all freed. He and Valentine won't have an army, the demons are gone, and Jonathan's not half demon anymore."

"If he lays a hand on one of my brothers," Isabelle vowed, "I'll kill him."

"He can't hurt Max as long as they're in the Tardis-"

"_Clary_?"

Clary's eyes jerked irresistibly away from Isabelle to the lone figure standing in a circle of other shadowhunters. She knew that woman, though it was from a distance, like she were looking at a person long dead. Still, those green eyes, that red hair; it was Jocelyn, and she looked both furious and terribly sad.

"Mom," Clary said formally, and she felt Isabelle move a bit closer to her.

"What have you done?" Jocelyn asked, eyeing the Cup. "Where is Jonathan? Where is Valentine?"

"Is he all you care about?" Clary demanded, her eyes flaming. "After everything he's done, after all the people he's hurt you only want to know that he's alright?"

"He's my husband," Jocelyn said evenly. "He's the father of my children. What do you expect from me?"

"To love me," Clary said desperately. "What about me? I'm your _daughter_!"

The Doctor, who had seen the woman emerge from the crowd and call out Clary's name stirred from his spot. He sensed the anger boiling. "What are you two arguing about now?" he asked loudly, stepping between the two women. Jocelyn eyed him with mounting dislike.

"Who are you?" she snapped, and then her eyes widened with understanding. "You're the man who stole my children!"

"Stealing is an extreme word," the Doctor said, smiling ruefully at her.

"You abducted Jace and Clary out of school, and then, you came back for Jonathan!" Jocelyn's face was turning bright red, and Clary saw her hand going for a blade at her hip. "I should kill you," she said softly.

"Mom," Clary said, and she stepped before the Doctor, blocking him from her mother's wrath. "I _left _with him; Jace and I ran off."

"He took you-"

"_No_!" Clary cried, stamping her foot. "Listen to me! We left, we left Valentine, Jonathan, and _you_ because we hated it there. I don't know what spells he used, I don't know how he lied, but Valentine is a monster. He was hurting me and Jace, and no one there seemed willing to help or even care." All those months of silence were finally tearing free and Clary found she couldn't stop the words pouring out. "You just stood there and you watched us while Valentine hit us, and burned us, and made us do horrible things, but nothing mattered to you except that he loved you."

"I wanted you to be happy!"

"I was _miserable_!" Clary snarled. "You knew I was and you just didn't care. So, yes, Jace and I ran off. We met the Doctor and the Ponds," Clary gestured at the Doctor and Amy and Rory, who looked back at her with serious, dark eyes, "and they took us off and I was finally _free_. I got to see things and do things I'd forgotten, and I wasn't afraid anymore. You've got no one to blame for all this but yourself."

It seemed like Clary was done, or she couldn't bear to look at her mother anymore; she spun about and found herself in the Doctor's comforting embrace. He rubbed her back and caught her eyes. "You were wonderful, Clary, and don't forget it. Now, let me handle the rest."

Jocelyn saw how Clary seemed so comfortable with the Doctor, and her heart constricted. "Let go of my daughter," she said warningly. "Take your hands off her, you monster!"

The Doctor held his hands up in surrender. "I think I can fix all of this if you'll let me, Jocelyn. I can help you clear your head up a bit, and it starts with you taking a drink from Clary's Cup."

"I won't be poisoned against the man I love," she hissed.

Amy lost her temper then. "Then do it for your daughter! My god, what kind of mother are you, that you'll let your daughter hate you and not try to fix it? She's your daughter-your _only _daughter-you should be willing to go to the moon and back for her. I know I am!"

Jocelyn frowned at Amy, but she wasn't nearly so foreign as the Doctor, and she seemed a bit more real, a bit more trustworthy. Slowly, her eyes moved to the Doctor. "I should kill you, but I won't," Jocelyn said, looking at the Cup with suspicion. "If this is the only way to make my daughter trust me again, I'll drink from her Cup. Then, when Valentine arrives, he'll kill you."

The Doctor took the Cup from the shadowhunter sipping from it and offered it to Jocelyn with a flourish. "I look forward to it."

"Glad to hear it, Doctor," said a smooth, polite voice.

Everyone froze as Valentine and Jonathan came into view; Clary, especially, seemed sick with fright when she saw Jace bound and Max in Jonathan's arms. "Let them go!" Clary shrieked, her eyes on Jonathan.

Jonathan smiled widely at his sister. "Now, now, let's not get ahead of ourselves."

"Clarissa," said Valentine, and his eyes gleamed at the sight of his daughter positioned between the Ponds and the Doctor. "I should have known you'd do something like this, though I didn't think you _could_."

"I guess I had a bit of help," Clary ground out, but her eyes were locked on Jace's. He looked faintly ill and his lips were pulled back in a perpetual snarl. When he saw Clary watching him, his face softened just a little. "Let Jace go."

Valentine shook his head sadly. "I don't think I can do that, Clarissa. The last few days, you've run quite amok. I've heard stories about things, and I can't say I'm too pleased with them. It's time this nonsense ended."

Max chose then to give a shill cry and he started kicking at Jonathan. Jonathan gave a furious grunt and dropped Max; the boy landed, clearly dazed by the fall. "I'm tired of toting your brother around!" he snapped at Isabelle and Max. "No wonder I killed him."

"Don't you touch my brother!" Isabelle howled, and she got a few threatening steps forward before Alec and Magnus managed to catch hold of her and pull her back.

"Jonathan, be gentle with the boy," Valentine said coolly. "We don't want to kill anyone; that's why I summoned the Angel in the first place."

"Speak for yourself," Jonathan muttered, and he caught Jace's eye. Jace saw that odd glint in Jonathan's eyes again, and he wondered what was going through the other boy's mind.

"I have come to put this rebellion to an end and bring peace once more to the shadowhunters. Jocelyn, put aside the Cup and come with me. Clarissa, get away from that _thing_." His eyes alighted on the Doctor, sneering, but the Doctor wasn't looking at Valentine.

No, after a closer inspection, Valentine noticed the Doctor was eyeing Jonathan closely. "Jonathan," said the Doctor, "you don't have to do this. I know you think you're trapped by your past, but I promise you, you're not. Look at me, look what I've done, and here I am."

Jonathan's eyes narrowed. "I don't have a choice. I don't get to just run off when things go sour and explore the universe. I've got a life to live here."

"Listen to me," the Doctor said desperately, and he reached out his hands pleadingly. "It doesn't have to end like this; you can change that. You, Jonathan, you're amazing, you're brilliant, you're wonderful, and all you have to do is give it a moment's thought."

A dark smile slipped across his face, and Jace noticed that he seemed detached; any glimmer of light, odd or otherwise, was gone from his face. "I've given it all the thought it needs, Doctor. This is the only way I can have a life, the only way I get justice."

"That's what you want? Justice?" the Doctor rasped. "There are more important things than justice, Jonathan."

"Be quiet!" Valentine ordered. "Jonathan is my son, and unlike my daughter, he will follow me. As soon as this coo is put down, I'm going to finish you off, Doctor."

The Doctor seemed completely unfazed by Valentine's threats. "Please, Jonathan, it's not worth it."

"Don't you _understand_?" Jonathan hissed. "For the rest of my life, I would be known as _Valentine's Son_. Do you think I want that? The hatred of my fellow shadowhunters? No, this is the only way I can ever be something other than Valentine's Son."

"Traitor!" Isabelle cried.

"Monster!" Alec growled.

Jace, unable to speak, settled for a furious glare. Only Clary was watching Jonathan's eyes now, and what she saw there confused her. He caught her eyes and his lips quirked up.

"That's not true," the Doctor pressed. "I can help you, Jonathan. Let me help you."

"No thanks, Doctor," Jonathan snorted. "I think you've helped about enough. I'm ready to do this all on my own."

Valentine placed a cool palm on Jonathan's shoulder. "So long as I'm their leader, you can be whatever you want to the shadowhunters."

Jonathan smiled up at his father. "I know that, Father, but you'll have to forgive me."

"Forgive you what?"

"What I want to be," Jonathan answered simply.

"Jonathan!" the Doctor cried one last time, but it was unheeded.

Valentine frowned, speaking over the Doctor. "And what is that?"

There was a perceptible, thoughtful pause, while Jonathan seemed to consider his options and the Doctor made a move toward him and Clary noticed the grim look on her brother's face. There was a pause, and then Jonathan moved. Light flashed off a blade, a small dagger, and the next moment, Jonathan had buried the blade of the knife deep in Valentine's back, smirking ever so slightly when he saw the politely surprised look on his father's face. After a few seconds, a dot of blood blossomed on Valentine's chest, expanded, and then began to dribble down his front.

Jocelyn gave a terrified cry and rushed forward, dropping the Cup. She pushed Jonathan aside and he stumbled a bit, staring at Valentine's slouched, lifeless form. He had severed his spin and priced his heart at the same time-exactly the same way he should have died. Jonathan landed, dazed, beside Jace, and slowly looked up at the other boy. Jace was looking at him with the most confused expression he'd ever worn.

The Doctor gave a frustrated cry before spinning away, pulling at his hair. "Jonathan!"

Clary felt herself shaking, and for the first time, she want to run at Jonathan, not to hurt him, but the gather him up in her arms. He looked almost as shocked by his own actions as Jace did. Isabelle and Alec were staring, open-mouthed, at him, like he were some strange animal. Clary took a few tentative steps toward her brother, and finally went to his side. His crooked smile looked rueful and full of bitterness.

Brother and sister shared a long, telling look. Clary knelt down beside him and touched his shoulder. After a complete minute where Jonathan and Clary looked into each other's eyes, Clary finally spoke. "I'm not mad, I'm just…_Why_?"

"It was the only way," Jonathan finally said, shrugging off the looks he was getting from the small, assembled group. "So long as Valentine was alive I would always be Valentine's Son. At least now, I can be the man who murdered Valentine. At least now, I'm free."


	20. Epilogue: Five Years Later

**So, this is it! I hope you all enjoyed my first try at a crossover. Thanks for reading! **

Epilogue: Five Years Later

_This is just one corner of one country in one continent on one planet that's a corner of a galaxy that's a corner of the universe that is forever growing and shrinking and forever creating and destroying and it never remains the same, for even a single millisecond, and there is so much, so much to see. Because it goes so fast._

_-The Doctor_

Clary watched the blazing setting sun sink below the line of towers and buildings that composed the New York City skyline through her apartment window. It was stunning, breathtaking in its usual way, but it didn't really impress Clary anymore. She rolled over onto her back and stared up at the ceiling, letting the sound of the city drown out her restless mind. As usual, though, it was only replaced with the whooshing sound that had been haunting her dreams.

Five years ago, Clary, Jace, Jonathan, the Lightwoods, Magnus, the Ponds and the Doctor had finally stopped her father, and even now, it seemed unreal. She had watched, awestruck, as Jonathan drove a knife through her father's spine, killing him instantly, and suddenly, all the misery and pain that had plagued her and Jace for months was gone. In that ensuing chaos, Jocelyn had gone into a wild panic and had needed to be pulled away by nearby shadowhunters and sedated by Magnus. It would be a long time before Jocelyn would speak to anyone, and even longer before she agreed to drink from the Cup.

Clary, though, had remained in the center of the city, staring in shock at her dead father and listening to the Doctor, ranting at Jonathan, pleading uselessly, like it had all gone wrong. It had taken a bit of time for Clary to realize that the Doctor hadn't wanted _anyone _to die, not even Valentine. She didn't quite understand that, but, she figured, he had seen more of life and death than anyone else, and maybe he just got tired of it. Regardless, Clary had promptly tugged the gag free from Jace's mouth and kissed him firmly in celebration.

The rest of the events of that day seemed like a movie on fast-forward, five years later, she still couldn't quite recall how she had found herself in a bed that night, snuggled against Jace's side. She remembered the shadowhunters rejoicing, she remembered Robert and Maryse running forward, tears streaming down their faces as they joined their children and Jace, she remembered Luke and Simon emerging from the crowd, looking pale and tired, but safe, and she remembered that feeling of elation that came with her freedom.

Someone, Amy most likely, had led her away from the crowds and the questions and the rather gruesome scene of her dead father, and into the Gard. Clary had sat there alone for some time before she heard the door open and the sound of footsteps echoed about her; expecting Jace, she leaned back against a wall and closed her eyes.

"All quiet on the western front?"

"Not really." Clary jerked up at the sound of Jonathan's voice. He came forward, hands in pockets, face down; when he was at her side, he looked at her. "I suppose I have some explaining to do."

Staring at her brother's open, contrite face, Clary felt the first stirrings of empathy she'd ever felt for Jonathan. "No, you don't. I'm not upset, I'm not even angry; I'm glad you did what you did, for whatever reason you did it."

"I did it for myself," Jonathan said evenly.

Clary simply shrugged. "Whatever the reason, it's done now."

"You're not worried I'm going to go back on my word and kill everyone?" Jonathan eyed her closely. "Not worried I'm going to hurt Jace? Max?"

A shudder raced up Clary's spine. "The Doctor said you wouldn't, and you didn't. I figure I should just trust his judgment from now on."

Jonathan nodded his head, considering. "How long do you think it's going to take for all this to settle down? I'd like to be gone before everyone knows what happened."

"I thought you wanted to be remembered as the man who killed Valentine?" Clary asked.

"I do," Jonathan agreed, "but I don't want to be here to be remembered. I might go back to New York. The apartment is still open."

For some reason, the idea of Jonathan living alone in that huge, spacious apartment upset Clary, but she was saved responding by the sound of her name being called. "Clary? Clary are you in here?"

"Jace!" Clary called back, moving a little toward the voice. Jace emerged and Clary rushed into his arms. "How are things out there?"

"Well, the initial surprise is gone, but there are still a lot of questions. The Doctor has conveniently vanished, so people have been asking me." Jace looked annoyed. "It's not like I can explain what happened."

"Told you we should go soon," Jonathan said softly, drawing Jace's attention his way.

"I was wondering where you'd gone off to," Jace said quietly.

"Still want to kill me, I suppose?" Jonathan asked sardonically. "Plenty of time to do it now, no one will stop you." Almost unwillingly, Jonathan's eyes flickered to Clary.

Jace titled his head, viewing Jonathan speculatively. "I don't want to kill you."

"Really? That's certainly a pleasant change," Jonathan snorted. "I suppose I must concede to you my undying gratitude?"

"Keep your gratitude," Jace said indifferently, and then, though it sounded painful for him to say, "You've done more than any of us could have hoped for; we're all grateful." Jace wrapped his arm around Clary's waist and made to pull her off to go find the Lightwoods, but Clary dug her heels in.

"Where are you going?" Clary asked Jonathan, unable to just leave her brother.

Jonathan's eyebrows raised. "To New York, for now. I'll stay in the apartment as I don't think I'm very welcome at the Institute."

Clary wanted to say that wasn't true, but she didn't think Isabelle was going to let Jonathan within a mile of her brother. "Well, you know how to contact me if…you need anything."

For a moment, Jace wanted to tell Clary off, but he couldn't forget that through it all, despite everything he had said, Jonathan had turned out to be truthful. He couldn't forget the things he had said either. "We'll be heading back to New York soon, too. You know where to look for us."

"I might just do that," Jonathan said and tipped his head before Jace led Clary away and back to the Lightwoods.

That night, unable to bear the searching eyes and questions, Clary and Jace went to find the Doctor and the protection of the Tardis. It was right where it had been left, somehow overlooked in the chaos that was ensuing in the city proper. She knocked on the door, but on her second attempt, the door opened on its own, and they entered, the familiar thrumming of the Tardis soothing to their senses.

"Jace! Clary!" the Doctor cried, coming down the steps, his arms thrown wide. Amy and Rory and River came tumbling down after him. "Look at you two!"

Clary smiled shyly, leaning against Jace. "We came to say thank you and-and…" it was then that Clary saw the screens of the Tardis. They were flashing with maps of stars, the buttons blinking just like they had right before the Doctor threw the Tardis into the time vortex, and the Tardis seemed to be groaning in anticipation. "Are you leaving?"

The Doctor smiled sadly, and it reached his eyes. "Clary, it's time for us to go before people start really asking questions."

"You can't go," Jace said, and Clary was surprised to hear how desperate Jace sounded. "You have to help us fix the Clave and-and meet out families and-"

The Doctor held up his hands. "Jace, Clary, you have to understand," he said softly, "I'm not the type of person to hang around very often. There's so much to see, so many other people to help, and this is just one stop in the thousands I've got to make."

"We need you," Clary whispered. "You've helped us so much but we can't do the rest on our own."

The Doctor took both Jace and Clary by a shoulder and pulled them in. "You have no idea what you can do on your own."

"We don't want you to go," Jace finally said, realizing he was sounding like a small child.

"It's not really a choice," the Doctor sighed. "I've got other places to go, other people to see, and so many other adventures to have."

Clary and Jace knew by the finality in his voice that the Doctor was set and that he was going to leave. It was then that Clary realized that she and Jace and all their friends had only been _one_ adventure in the Doctor's thousands; they were simply a passing faze of his life. Her eyes landed on Amy and Rory, looking uncomfortably at them, and she knew how foolish she had been. The Ponds were enduring fixtures in the Doctor's life and she was fleeting; vaguely, she wondered what it meant to be a companion to the Doctor, to be one of the lucky ones who got to set off with him into the stars. Her heart beat painfully.

"Goodbye, Doctor," Clary finally said, and then she hugged him tightly against her. "Thank you _so much_, for everything."

"It was a pleasure," the Doctor demurred, and then moved over to Jace, who shook his hand. "Jace, I trust you'll be looking after this little girl?"

"Always," he said.

Amy and Rory came down and Amy kissed Clary's forehead. "You just stay out of trouble, alright? No more wars, no more magic cups, just settle down with that boy of yours."

Clary smiled through tears. "I don't know about the first two, but I'm not planning on letting Jace out of my sight.  
"Good girl," Amy said, and hugged her one last time.

Rory went over to Jace and gave him a fatherly squeeze on his shoulder. "Keep up the good work, Jace."

"You too," Jace said, recalling the first time he had met Rory, the first time he'd trusted him enough to let him help. "I'd say I'll see you around, but I figure I won't."

"One can only hope not," River said, giving both the children a small smile. "I don't think the universe can handle us turning up in this century again."

And that was how they left it. Clary and Jace left the Tardis and the door closed. They stood, holding onto each other, while they heard that earth-shattering groaning, the lights flashed, and slowly, the Tardis disappeared. For a long time afterward, Jace and Clary stood there, feeling a bit emptier, and a fair bit sadder, than before.

After that, they returned to the Lightwoods, who announced they were leaving Idris the following day. Clary and Jace spent a night in bed and the next morning, Magnus made a portal, and they left the Glass City. Jocelyn remained behind, having refused to drink from the Cup, and so, when Clary and the Lightwoods returned to New York, she moved into the Institute. Word reached her that Jonathan was living in the old pent house, and she and Jace would meet with him often, just to see how he was keeping up. It was almost a year later when Jocelyn finally agreed to drink, but by that time, Clary had lost almost all hope of her mother.

Without a home to return to, Clary stayed at the Institute with the Lightwoods for another year before Jace turned eighteen and found an apartment for them. Now, five long years later, Clary and Jace were still living together happily. But every year, the longing got worse, and she thought more and more of her short time on the Tardis. Clary wondered what would have happened if she had asked the Doctor if she and Jace could go with him, but then another part of her mind would say that she belonged here, in New York, with her friends and family and the ground firmly beneath her feet.

"Clary, Clary, you ready to go? Isabelle is going to throw a fit if we miss her twenty-first birthday dinner." Jace was standing the door frame, smiling at her; he knew that look on her face, and he knew what she was thinking.

Clary sat up, brushing wrinkles out of the dress she was wearing. "Throwing a fit is putting it lightly. Where are we going?"

"Some club, then we're having dinner at Taki's," he shrugged. "Of course, even if we're a few minutes out it won't compare the Magnus and Alec, those two make a point of being late."

"I think that's Magnus's influence," said Clary, and she sat up and swung her legs around the bed, touching the floor delicately. "He's corrupting our Alec, you know."

Jace grinned and came up behind Clary and the two stood before the mirror in their room. Clary was in dark green and strappy heels, and, inspecting herself, she decided that five years hadn't done much for her appearance. She was still short, still petite, and still freckled; it was only under close inspection that Clary saw the differences. Her hair was a few shades darker, the curls less tight, her cheek bones a bit more pronounced, and her body more shapely. Her eyes moved over to Jace, standing behind her, and she frowned. He would always look the same: unbearably handsome.

For Jace, though, there was no better sight than Clary. He never cared how she looked, what she wore, or what she did, Jace only ever had eyes for her. He wrapped his arms about her waist and kissed her neck. Slowly, one of his hands moved down her arm and to her wrist, his fingers twining in hers, fiddling with the small ring he had given her.

"When are we going to tell your mom?" Jace whispered, smiling against her cheek.

Clary blanched. "She won't care; after everything that happened, all she wants to do is make me happy. But, still," Clary said, considering the formidable argument she might soon be faced with, "maybe we should enlist John," she said, using her brother's preferred name.

"We'll mention it to him tonight," Jace said decidedly. "He's coming, isn't he?"

Clary grinned wickedly. "Isabelle made a _point_ of inviting him."

Jace raised an eyebrow. "Getting serious, is she?"

It was true that Clary's relationship with John had grown and flourished until she was comfortable calling him her brother. Through Clary, Jace and the Lightwoods quickly came around to John, though they had remained distant for almost three years. John had spent the first few years living in the pent house, mostly keeping to himself, but visiting with Clary and his mother. During that time, he had come to adopt the name John instead, and had insisted they call him that.

Sometimes during the fourth year, John had suddenly emerged from his loneliness, and had asked to be a part of Clary's life. She had agreed, thinking the best she could do for him was be welcoming and warm. It was then that he became a more permanent fixture among Jace, Clary, Isabelle, and Alec. His seclusion had wrought changes in him, and now that bitter fire that had burned in John had simmered out. He was often quiet, given to long thoughtful pauses, and he was careful to judge any situation as he believed firmly in what was just.

There were some who were still scared of him, but John's hope of being remembered as the man who murdered Valentine, had been met. Since Clary and Jace could not tell anyone the truth of the Doctor and the Ponds, they had quickly spun a story where John was the unwilling hero. They said that during the months they lived with Valentine, John had opened up to Clary and Jace, and, feeling protective over his siblings and angry with Valentine, he helped Clary and Jace escape, freed the Lightwoods, and together, they engineered the plan that culminated in John killing Valentine. He had become a hero, famous among the shadowhunters, there were even rumors that he was being asked to be the next Inquisitor, but he still preferred to live outside the city.

Lately, Isabelle had made a point of visiting with Clary and Jace while John was over. Much of her anger that had been directed at him for attempting to kill her brother had fizzled out. She had grudgingly admitted that since it never actually happened, she couldn't be angry about it. John had listened to her explanation of her anger with a blank face and when she had finished, he had simply bowed his head and moved on with his life.

Now, Isabelle seemed constantly interested in what John was doing. She would ask after him from Clary and Jace, make sure he knew he was welcome with them on their nights out, and had even gone as far as to call him herself when she planned her birthday party. Clary found it oddly touching that Isabelle was warming up to her brother.

"I think Isabelle is just tired of John ignoring her," Clary laughed and then nudged him. "Come on, I don't trust her alone with my brother."

Jace and Clary left the apartment and were soon arriving outside the club Pandemonium. They slipped in easily and were soon engulfed in the music and crowds. As usual, Jace was getting the lion's share of attention, but recently, Clary had begun to dress up, and men had been taking notice. Jace found this most annoying, and he had taken to walking with his arm firmly about her; Clary thought it was funny he was jealous.

It was this way that Clary and Jace found Isabelle, seated at a booth, a drink in her hand, and none other than John seated at her side. When he saw Jace and Clary, he moved over, making room and bringing himself within Isabelle's reach. She seemed pleased with this, and smiled about at all the other women in the club, as if daring them to come over. Jace rolled his eyes and winked at Clary.

"It's about time you two showed up," Isabelle said crossly. "Is John the only person here who believes in being on time?"

"He's the only one who cares," Jace muttered, and he saw John smirk into his drink. "Where's Alec and Magnus?"

"Probably necking somewhere," Isabelle sighed dramatically. "I don't know why they're not married yet. They've lived together for years."

"Alec can't get married until I've approved the relationship," Jace said importantly. "After all, I'd be the best man, my opinion matters most."

Isabelle snorted. "Speaking of weddings, when do you two plan to make that announcement?"

"I need to speak with you about that, John," Clary said. "I think Mom is going to freak if I tell her."

"You're not wrong," he said, eyeing his drink. John was the only one who still kept up a regular correspondence with Jocelyn. "After everything, she thinks women should be single forever. Marriage is an institution from hell."

"That, and Macy's, which I can only assume is where you bought that disgusting shirt, John." It was Magnus, and he was leaning over the edge of the booth, eyeing them all up. "Really, brown?"

"Magnus!" Isabelle snapped, as she had been admiring the cut of the shirt before. "Where's my brother?"

"Getting my drink. Shove over, Jace," he added, and sank down, grinning his usual, dark grin.

"As Alec's parabatai-"

"As Alec's _boyfriend_, I take priority," Magnus said loudly, and winked at Clary. "Ah, and here he comes now."

Alec emerged from the crowd, holding two glasses. He smiled guiltily at Isabelle and then joined Magnus. He was the same as ever, though the planes of his face were more handsomely defined, and he spoke more often now. "Sorry we're late, Izzy."

"Yeah, sure," she said.

The group settled together and as one, they toasted Isabelle's twenty-first birthday. For the next few hours, they fell into comfortable conversation, shouting over the music and teasing gently. At one point, after having consumed a large amount of alcohol, Isabelle dragged Clary out onto the dance floor, casting provocative eyes at both Jace and John. The boys were content to sit and sip their drinks, but when Jace turned to mention something to Alec, he found that Alec was quite busy with Magnus, and gave John a brave look before moving out onto the dance floor with Clary. Eventually, John joined them, looking like his usual cool, collected self, but Isabelle caught his hand and pulled him into a dance. The night ended soon afterward, though, when Isabelle said she was starving.

They left Pandemonium then, Alec and Magnus walking so that they were touching up and down their sides, Clary holding Jace's entire arm, and Isabelle, wobbling in her heels and using John as her personal walking aid. They arrived, loud and laughing, at Taki's and managed to slouch into a table and order a number of entrees.

"How's Max?" Jace asked around a mouthful of French fries.

"He's started training," Isabelle said. "Ugh, he's fourteen you know? We're all so _old_!" She snorted at her own joke, which rose up a round of laughing. "He says he wants to be just like you, Jace, and all he wants to do is train."

"Admirable," Jace nodded, but his seriousness failed when Clary, tipsy, tried to rest her elbow on the table, missed the table, and collapsed on his lap.

For a while, they laughed and ate, and slowly sobered up. When they left Taki's it was late and sky was clear. Clary hung back, holding onto Jace for support and stared up at the night sky. Those stars, those glowing bring stars, were so far away. But they didn't have to be. She remembered the stardust in a jar and watching space stretch out before her like an endless void. Suddenly, this world, this place, just wasn't enough. All she wanted was to keep going and going…

"We should have left with him," Clary said softly to Jace, and she didn't need to tell him who she meant. "Every day I miss him, and every day I wonder what would have happened. Every day I feel like this life just isn't _enough_."

"I know what you mean," Jace admitted. "I keep wishing I'd hear that whooshing sound and feel the wind move and see the Tardis come into view. I wish he'd just turn up like before, out of thin air-"

Jace's words were cut short and his heart stopped. The wind around them suddenly picked up and tossed their hair about, and then, from a distance, they heard the grinding of gears, the groaning of a tired machine, and the whooshing of space. Clary's mouth hung open and she stared up at Jace, wonder and hope mingling on her face.

"You don't think…?"

Jace took off before he could stop himself and Clary right on his heels. They rounded the corner of an alley, and a gust of wind hit them both in the face. Clary held up her hands and saw a flashing light appearing in midair, and below it, the blue box that accompanied it. Jace skidded to a halt and gasped, grabbing Clary's arms and holding her against him.

"Clary, it's him!" he cried. "Clary, it's the Doctor!"

Clary felt tears prick her eyes and she gasped. The blue box stood before them, just the way they remembered it. It was as if five years had gone and past; it was like the Doctor had just stepped out for a minute. Slowly, Clary took a few steps closer, barely daring to breath. She stood a few feet away when the door creaked opened.

And out came the Doctor. He didn't look a day older, not even a minute older. His hair was still big, brown, and uncontrollable. His eyes were still green and bright with memories. His face was still boyish and sweet. And his clothing…still the silly coat and button shirt, the suspenders, and that _ridiculous _bowtie. The only thing that seemed to be missing was that sweet smile; his face was completely serious, completely blank.

"Doctor!" Clary cried, and she rushed at him. In a moment, he broke into a grin and he caught Clary and hugged her close. "Doctor, you're back. Jace, he's back!"

Jace came pelting along the alley and was soon beside the Doctor. "What brought you back?"

The Doctor looked between them and saw the marked differences in their appearances, not to mention the ring on Clary's finger. _So, he's proposed. The Tardis said the engagement was confirmed…_ "Well, I've been a bit bored lately, and I thought I swing through and see if the world was falling apart again."

Clary and Jace laughed. "No, it's just normal."

"Boring," the Doctor muttered, and took a few steps about, as if inspecting the place. "You like it? Boring and all?"

Jace frowned, ignoring the Doctor's comment. "Where are Amy and Rory?"

Here, the Doctor came to a sudden halt, his muttering stopping, and spun about to face Jace. "What?"

"Where are Amy and Rory?" Jace repeated, looking back at the Tardis. "Did they want to stay home or something?"

The Doctor's face, and all its cheerfulness, fell. "Amy and Rory are…well, they're-they're gone," he finally admitted, and then fell against the nearest wall like he were limbless.

Clary's mouth opened wide and she too looked toward the Tardis. "They're dead?"

"Well, when I left they weren't," the Doctor grunted. "Though, seeing as it's 2012, they're dead at this point."

"What do you mean?" Jace asked gently, sensing a great fissure of pain in the Doctor.

"We were attacked…the Angels…Rory was trapped in the New York in the 30's and Amy couldn't leave him. She went back, but I'd done so much damage to the time stream that I couldn't go back…" The Doctor closed his eyes. "I just wanted to swing through, visit the city and pay my respects, and the Tardis brought me here."

Clary was covering her mouth and she heard Jace's sigh beside her. "Always where you need to be," he said.

The Doctor looked up sharply at that. "How long have I been gone? How old are you two now?"

Jace spoke since Clary seemed beyond speaking. "I'm twenty-two and Clary will be twenty-one in a week or so. Why?"

The Doctor didn't answer but gave him a long, considering look. "How's Jonathan-?"

"Jace!" It was Isabelle. "Clary!"

"Where are you guys?" Came the familiar voice of Alec.

They heard footsteps in the distance and their group of friends arrived on the scene. There was a perceptible pause while everyone stared at the Doctor, leaning against the wall of grimy building as if wounded and the Tardis waiting, door open. Isabelle suddenly gave a shout and threw her hands in air.

"Doctor!" she cried, and rushed down the lane. She was closely by Jonathan, Alec, and Magnus. "What are you doing back here? We thought you'd be gone forever."

"No, I'm just…passing by," he said, and his eyes alighted on Jonathan. "And how are you, Jonathan?"

"It's John now, and I'm well," he answered, and he meant it.

"Good then," the Doctor said, and then strolled back toward the Tardis, pausing to take another glance. "Well, yes, like I was saying, I thought I'd just stop by on my way out, see how you all were doing. All just leading your boring lives I guess…bit boring here, really…"

Clary, who was still in slight shock over the death of the Ponds, saw the way he fiddled with his bowtie. "Well, it's not _all_ boring," she said, but she felt oddly elated and she didn't know why.

"Yeah, of course!" he said suddenly, nodding his head. "Just living in New York, no demons, no fights. Must be nice to lounge around."

"I suppose you don't do any of that up in space?" asked Isabelle, wondering why the Doctor was biding his time with the stop.

"No, it's always an adventure. Every day is an adventure on the Tardis, but I don't think you'd be interested in that. I mean, you're engaged, must be busy with all that…"

Clary and Jace looked between each other. Finally, Clary spoke. "Are you inviting us to…go with you?"

The Doctor jumped as if he'd been stung. "Come with me? Well-I mean-if you _wanted_ to come with me, I wouldn't say no. But, you know, only if you have the time and-"

"Of course we want to come!" Clary cried, springing at him with gleaming eyes. And caught up his hands and tugged. "Jace, you want to go, don't you?"

Jace looked blankly from the Lightwoods to the Doctor. He swallowed loudly and said, "Y-yes, of course I want to go."

The Doctor's eyes lit up and a smile split his face. "Really?" he asked with a boyish smile. "You want to come?"

Clary laughed at his surprise. "Yes, yes, yes!" she cheered. "I've been thinking about this, dreaming about this…" Her eyes were glowing and she turned to Jace, who was smiling faintly, but his eyes turned on the others.

"I know you're probably thinking-"

"Go with him, Jace," said Alec, who was watching the Doctor closely. "I mean, how often are you going to get the chance for something like this? We'll be here waiting for you, don't worry."

Jace nodded and saw Clary pull away from the Doctor. She was looking at John. "You'll be alright?"

John smiled. "I think I can manage without our lunch dates, little sister."

Clary embraced her brother, clinging tightly to him, and then rose on tiptoe and said in his ear, "Why don't you stop stringing Izzy along and just give her what she wants?" Then she giggled at the look of surprise on his face and turned to the others. "Don't worry, you guys, we'll come back and visit. I mean, it's a time machine, we can be back tomorrow!" Isabelle smiled and kissed Clary's cheek. "Just-just make something up about us, why we're gone, you know? I don't care, we'll still come back for you."

"You take care of them, Doctor," Isabelle warned, and then stepped back.

Jace hugged each of his friends in turn and then took Clary's hand in a strong grip. The Doctor came up beside them and smiled down on them, and in his eyes, they saw a bright light, like hope.

"We've been waiting a long time for this," Clary said, and then faced the Tardis.

In they went, the Doctor, Jace, and Clary, into the Tardis. The Doctor was off like a shot, telling them places they could go, times they could visit, planets that were left to be seen. Clary was staring around in wonder, her memories of the Tardis coming back in a heartbeat, and beside her, Jace was shaking with excitement. The Doctor was throwing switches, pushing buttons, screaming things at the Tardis like he were arguing with it. He finally turned back to them and clapped his hands.

"Right, what do you earthlings want to see?"

Clary smiled wryly and Jace kissed her hair. She said, "Show me the stars."

**The End**


End file.
